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Commit id: 652bb7c24e092a61c71765d9ae2de1e384b1c408

update vignette to add example of merge_tree <2015-04-29, Wed>


Commit id: ac252d451f6b2e5b0d27c055e050e1e42a6ffe56

add examples folder in inst that contains sample data <2015-04-29, Wed>


Commit id: d3bb757a48866f960e5c3b5c4da088241a410deb

in addition to parsing beast time scale tree in XXX_year[\\.\\d]*, now supports XXX/year[\\.\\d]*


Commit id: 33d9f8a12db641fe8580a20e3a2b51f4798fd96f

update gplot, now rowname of heatmap will not be displayed <2015-04-28, Tue>


Commit id: 94b64487871856f3394ed53d1ab55a4b6abc0baa

add line break if substitution longer than 50 character <2015-04-28, Tue>


Commit id: 396f41d759d1eb1ffa2b8af9d1b9eda695afe110

support calculating branch for time scale tree


Commit id: 0ba9f78c1626ec0fa1c503ac8b6f50e363976586

update vignette


Commit id: 5510c5f96044238cdeca127c9514b9a02851ecdb

remove parsing tip sequence from mlb and mlc file <2015-04-28, Tue>


Commit id: fc375e2b9825d840855c6276cf4301802f3e5bdc

o remove tip.fasfile in read.paml_rst for rstfile already contains tip sequence <2015-04-28, Tue>


Commit id: 03109db58c26037aeab23dbaf372638edbad5f67

scale_color accepts user specific interval and output contains scale attribute that can be used for adding legend <2015-04-28, Tue>


Commit id: 7c5829cfa47d36db179fd8b0c089a5c4f34ff345

extend fortify methods to support additional fields <2015-04-28, Tue>


Commit id: 1b0d72edd2f8e299b56296bc6066259a682128ad

extend tree class to support additional info by merging two tree <2015-04-28, Tue>


Commit id: a8b2f5480b31e0bef233e0483966afc4ea5ef9d6

extend get.fields methods to support additional fields <2015-04-28, Tue>


Commit id: 70831ecc379dbfc6f77cd1373d3a0e03241bbf4d

implement merge_tree function to merge two tree objects into one



git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@103244 bc3139a8-67e5-0310-9ffc-ced21a209358

g.yu authored on 29/04/2015 10:37:43
Showing 31 changed files

... ...
@@ -1,7 +1,7 @@
1 1
 Package: ggtree
2 2
 Type: Package
3 3
 Title: a phylogenetic tree viewer for different types of tree annotations
4
-Version: 1.1.1
4
+Version: 1.1.2
5 5
 Author: Guangchuang Yu and Tommy Tsan-Yuk Lam
6 6
 Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
7 7
 Description: ggtree extends the ggplot2 plotting system which implemented the
... ...
@@ -44,6 +44,7 @@ export(groupClade)
44 44
 export(groupOTU)
45 45
 export(gzoom)
46 46
 export(hilight)
47
+export(merge_tree)
47 48
 export(phylopic)
48 49
 export(plot)
49 50
 export(read.baseml)
... ...
@@ -112,7 +113,9 @@ importFrom(ggplot2,geom_segment)
112 113
 importFrom(ggplot2,geom_text)
113 114
 importFrom(ggplot2,geom_tile)
114 115
 importFrom(ggplot2,ggplot)
116
+importFrom(ggplot2,labs)
115 117
 importFrom(ggplot2,scale_color_manual)
118
+importFrom(ggplot2,scale_fill_discrete)
116 119
 importFrom(ggplot2,scale_fill_gradient)
117 120
 importFrom(ggplot2,scale_x_continuous)
118 121
 importFrom(ggplot2,scale_x_reverse)
... ...
@@ -1,3 +1,19 @@
1
+CHANGES IN VERSION 1.1.2
2
+------------------------
3
+ o update vignette to add example of merge_tree <2015-04-29, Wed>
4
+ o in addition to parsing beast time scale tree in XXX_year[\\.\\d]*, now supports XXX/year[\\.\\d]* <2015-04-29, Wed>
5
+ o add examples folder in inst that contains sample data <2015-04-29, Wed>
6
+ o update gplot, now rowname of heatmap will not be displayed <2015-04-28, Tue>
7
+ o add line break if substitution longer than 50 character <2015-04-28, Tue>
8
+ o upport calculating branch for time scale tree <2015-04-28, Tue>
9
+ o remove parsing tip sequence from mlb and mlc file <2015-04-28, Tue>
10
+ o remove tip.fasfile in read.paml_rst for rstfile already contains tip sequence <2015-04-28, Tue>
11
+ o scale_color accepts user specific interval and output contains 'scale' attribute that can be used for adding legend <2015-04-28, Tue>
12
+ o extend fortify methods to support additional fields <2015-04-28, Tue>
13
+ o extend get.fields methods to support additional fields <2015-04-28, Tue>
14
+ o extend tree class to support additional info by merging two tree <2015-04-28, Tue>
15
+ o implement merge_tree function to merge two tree objects into one <2015-04-28, Tue>
16
+ 
1 17
 CHANGES IN VERSION 1.1.1
2 18
 ------------------------
3 19
  o minor bug fixed in extracting node ID of rst file <2015-04-27, Mon>
... ...
@@ -18,6 +18,7 @@ setOldClass("phylo")
18 18
 ##' @slot tip.fasfile fasta file of tip sequences
19 19
 ##' @slot tree.file tree file
20 20
 ##' @slot ancseq.file ancestral sequence file, nexus format
21
+##' @slot extraInfo extra information
21 22
 ##' @exportClass hyphy
22 23
 ##' @author Guangchuang Yu \url{http://ygc.name}
23 24
 ##' @seealso \linkS4class{paml_rst}
... ...
@@ -34,7 +35,8 @@ setClass("hyphy",
34 35
              tip_seq     = "character",
35 36
              tip.fasfile = "character",
36 37
              tree.file   = "character",
37
-             ancseq.file = "character"
38
+             ancseq.file = "character",
39
+             extraInfo   = "data.frame"
38 40
              )
39 41
          )
40 42
 
... ...
@@ -60,8 +62,8 @@ setClass("hyphy",
60 62
 ##' @slot joint_subs sequence substitutions based on joint_ancseq
61 63
 ##' @slot marginal_AA_subs Amino acid sequence substitutions based on marginal_ancseq
62 64
 ##' @slot joint_AA_subs Amino acid sequence substitutions based on joint_ancseq
63
-##' @slot tip.fasfile fasta file of tip sequences
64 65
 ##' @slot rstfile rst file
66
+##' @slot extraInfo extra information
65 67
 ##' @exportClass paml_rst
66 68
 ##' @author Guangchuang Yu \url{http://ygc.name}
67 69
 ##' @seealso \linkS4class{codeml} \linkS4class{codeml_mlc}
... ...
@@ -79,8 +81,8 @@ setClass("paml_rst",
79 81
              joint_subs       = "data.frame",
80 82
              marginal_AA_subs = "data.frame",
81 83
              joint_AA_subs    = "data.frame",
82
-             tip.fasfile      = "character",
83
-             rstfile          = "character"
84
+             rstfile          = "character",
85
+             extraInfo        = "data.frame"
84 86
          )
85 87
          )
86 88
 
... ...
@@ -94,9 +96,8 @@ setClass("paml_rst",
94 96
 ##' @slot treetext tree text
95 97
 ##' @slot phylo phylo object
96 98
 ##' @slot dNdS dN dS information
97
-##' @slot seq_type one of "NT" and "AA"
98
-##' @slot tip_seq sequences of tips
99 99
 ##' @slot mlcfile mlc file
100
+##' @slot extraInfo extra information
100 101
 ##' @exportClass codeml_mlc
101 102
 ##' @author Guangchuang Yu
102 103
 ##' @seealso \linkS4class{paml_rst} \linkS4class{codeml}
... ...
@@ -107,9 +108,10 @@ setClass("codeml_mlc",
107 108
              treetext   = "character",
108 109
              phylo      = "phylo",
109 110
              dNdS       = "matrix",
110
-             seq_type   = "character",
111
-             tip_seq    = "character",
112
-             mlcfile    = "character"
111
+             ## seq_type   = "character",
112
+             ## tip_seq    = "character",
113
+             mlcfile    = "character",
114
+             extraInfo  = "data.frame"
113 115
              )
114 116
          )
115 117
 
... ...
@@ -121,13 +123,15 @@ setClass("codeml_mlc",
121 123
 ##' @docType class
122 124
 ##' @slot mlc A \code{code_mlc} object
123 125
 ##' @slot rst A \code{paml_rst} object
126
+##' @slot extraInfo extra information
124 127
 ##' @exportClass codeml
125 128
 ##' @seealso \linkS4class{codeml_mlc} \linkS4class{paml_rst}
126 129
 ##' @keywords codeml
127 130
 setClass("codeml",
128 131
          representation = representation(
129
-             mlc = "codeml_mlc",
130
-             rst = "paml_rst"
132
+             mlc       = "codeml_mlc",
133
+             rst       = "paml_rst",
134
+             extraInfo = "data.frame"
131 135
              )
132 136
          )
133 137
 
... ...
@@ -151,6 +155,7 @@ setClass("codeml",
151 155
 ##' @slot version version
152 156
 ##' @slot metadata metadata
153 157
 ##' @slot file jplace file
158
+##' @slot extraInfo extra information
154 159
 ##' @exportClass jplace
155 160
 ##' @author Guangchuang Yu \url{http://ygc.name}
156 161
 ##' @seealso \code{\link{show}} \code{\link{get.tree}}
... ...
@@ -164,7 +169,8 @@ setClass("jplace",
164 169
              placements = "data.frame",
165 170
              version    = "numeric",
166 171
              metadata   = "list",
167
-             file       = "character"
172
+             file       = "character",
173
+             extraInfo  = "data.frame"
168 174
              )
169 175
          )
170 176
 
... ...
@@ -183,6 +189,7 @@ setClass("jplace",
183 189
 ##' @slot translation tip number to name translation in beast file
184 190
 ##' @slot stats beast statistics
185 191
 ##' @slot file beast file, nexus format
192
+##' @slot extraInfo extra information
186 193
 ##' @exportClass beast
187 194
 ##' @author Guangchuang Yu \url{http://ygc.name}
188 195
 ##' @seealso \code{\link{show}} \code{\link{get.fields}}
... ...
@@ -195,6 +202,7 @@ setClass("beast",
195 202
              phylo       = "phylo",
196 203
              translation = "matrix",
197 204
              stats       = "data.frame",
198
-             file        = "character"
205
+             file        = "character",
206
+             extraInfo   = "data.frame"
199 207
              )
200 208
          )
... ...
@@ -96,7 +96,7 @@ setMethod("show", signature(object = "beast"),
96 96
               cat("...@ tree: ")
97 97
               print.phylo(get.tree(object))                  
98 98
               cat("\nwith the following features available:\n")
99
-              print_fields(object)              
99
+              print_fields(object)
100 100
           })
101 101
 
102 102
 ##' @rdname groupOTU-methods
... ...
@@ -150,7 +150,7 @@ setMethod("get.tree", signature(object="beast"),
150 150
 ##' @exportMethod get.fields
151 151
 setMethod("get.fields", signature(object="beast"),
152 152
           function(object, ...) {
153
-              object@fields
153
+              get.fields.tree(object)
154 154
           }
155 155
           )
156 156
 
... ...
@@ -12,9 +12,9 @@
12 12
 ##' mlcfile <- system.file("extdata/PAML_Codeml", "mlc", package="ggtree")
13 13
 ##' read.codeml(rstfile, mlcfile) 
14 14
 read.codeml <- function(rstfile, mlcfile) {
15
-    rst = read.paml_rst(rstfile)
16
-    mlc = read.codeml_mlc(mlcfile)
17
-    rst@tip_seq <- mlc@tip_seq
15
+    rst <- read.paml_rst(rstfile)
16
+    mlc <- read.codeml_mlc(mlcfile)
17
+    ## rst@tip_seq <- mlc@tip_seq
18 18
     new("codeml",
19 19
         rst = set.paml_rst_(rst),
20 20
         mlc = mlc
... ...
@@ -99,10 +99,8 @@ setMethod("get.subs", signature(object = "codeml"),
99 99
 ##' @rdname get.fields-methods
100 100
 ##' @exportMethod get.fields
101 101
 setMethod("get.fields", signature(object="codeml"),
102
-          function(object) {
103
-              fields <- c(get.fields(object@rst),
104
-                          get.fields(object@mlc))
105
-              return(unique(fields))
102
+          function(object, ...) {
103
+              get.fields.tree(object)
106 104
           }
107 105
           )
108 106
 
... ...
@@ -10,7 +10,7 @@
10 10
 ##' mlcfile <- system.file("extdata/PAML_Codeml", "mlc", package="ggtree")
11 11
 ##' read.codeml_mlc(mlcfile)
12 12
 read.codeml_mlc <- function(mlcfile) {
13
-    tip_seq <- read.tip_seq_mlc(mlcfile)
13
+    ## tip_seq <- read.tip_seq_mlc(mlcfile)
14 14
     dNdS <- read.dnds_mlc(mlcfile)
15 15
     
16 16
     new("codeml_mlc",
... ...
@@ -18,8 +18,8 @@ read.codeml_mlc <- function(mlcfile) {
18 18
         treetext = read.treetext_paml_mlc(mlcfile),
19 19
         phylo    = read.phylo_paml_mlc(mlcfile),
20 20
         dNdS     = dNdS,
21
-        seq_type = get_seqtype(tip_seq),
22
-        tip_seq  = tip_seq,
21
+        ## seq_type = get_seqtype(tip_seq),
22
+        ## tip_seq  = tip_seq,
23 23
         mlcfile  = mlcfile)
24 24
 }
25 25
 
... ...
@@ -79,7 +79,7 @@ setMethod("show", signature(object = "codeml_mlc"),
79 79
 ##' @exportMethod get.fields
80 80
 setMethod("get.fields", signature(object = "codeml_mlc"),
81 81
           function(object) {
82
-              object@fields
82
+              get.fields.tree(object)
83 83
           })
84 84
 
85 85
 ##' @rdname plot-methods
86 86
deleted file mode 100644
... ...
@@ -1,79 +0,0 @@
1
-
2
-merge_baseml_hyphy <- function(baseml, hyphy) {
3
-    ml_phylo <- baseml@mlc@phylo
4
-    hy_phylo <- hyphy@phylo
5
-    phylo_merge_check(ml_phylo, hy_phylo)
6
-}
7
-
8
-
9
-phylo_merge_check <- function(phy1, phy2) {
10
-    if (Ntip(phy1) != Ntip(phy2)) {
11
-        stop("Number of tip is not eqaul...")
12
-    }
13
-    if ( ! all(phy1$tip.label %in% phy2$tip.label)) {
14
-        stop("tip label is not consistent...")
15
-    }
16
-
17
-    if (phy1$Nnode != phy2$Nnode) {
18
-        stop("Number of node is not eqaul...")
19
-    }
20
-    if (!is.null(phy1$node.label) && !is.null(phy2$node.label)) {
21
-        n <- getNodeNum(phy1)
22
-        node <- (Ntip(phy1)+1):n
23
-        if (all(phy1$node.label == node) || all(phy2$node.label == node)) {
24
-            ## nothing happend.
25
-        } else if (any(phy1$node.label != phy2$node.label)){
26
-            stop("node label is not consistent...")
27
-        }
28
-    }
29
-    
30
-    degree1 <- table(phy1$edge[,1]) %>% sort
31
-    degree2 <- table(phy2$edge[,1]) %>% sort
32
-    if (length(degree1) != length(degree2)) {
33
-        stop("node degree is not consistent...")
34
-    } else if (!all(degree1 == degree2)) {
35
-        stop("node degree is not consistent...")
36
-    }
37
-}
38
-
39
-
40
-node_mapper <- function(phy1, phy2) {
41
-   df1 <- fortify(phy1)
42
-   df2 <- fortify(phy2)
43
-
44
-   df1$node2 <- NA
45
-   df1$visited <- FALSE
46
-   ntip <- Ntip(phy1)
47
-   df1$node2[1:ntip] <- match(phy1$tip.label, phy2$tip.label)
48
- 
49
-   root <- getRoot(phy1)
50
-   currentNode <- 1:ntip
51
-   while(any(df1$visited == FALSE)) {
52
-       pNode <- c()
53
-       for (i in currentNode) {
54
-           df1[i, "visited"] <- TRUE
55
-           j <- df1[i, "node2"]
56
-           ip <- df1[i, "parent"]
57
-           if (df1[ip, "visited"] == FALSE) {
58
-               jp <- df2[j, "parent"]
59
-               df1[ip, "node2"] <- jp
60
-               df1[ip, "visited"] <- TRUE
61
-           }
62
-           pNode <- c(pNode, ip)
63
-       }
64
-       currentNode <- unique(pNode)
65
-   }
66
-
67
-   if (df1[root, "node"] != df1[root, "node2"]) {
68
-       stop("phylogenies not compatible...")
69
-   }
70
-   
71
-   
72
-   node <- df1$node
73
-   names(node) <- df1$node2
74
-   phy2$edge <- cbind(node[as.character(phy2$edge[,1])],
75
-                      node[as.character(phy2$edge[,2])])
76
-   phy2$tip.label <- phy1$tip.label
77
-
78
-   reorder(phy2)
79
-}
... ...
@@ -22,9 +22,10 @@
22 22
 ##' colnames(d) <- paste0("G", 1:4)
23 23
 ##' gplot(p, d, low="green", high="red")
24 24
 gplot <- function(p, data, low="green", high="red", widths=c(0.5, 0.5), font.size=14) {
25
-    ## p <- p + scale_x_continuous(expand = c(0, 0)) + scale_y_continuous(expand = c(0, 0))
26
-    p1 <- p + theme(panel.margin=unit(0, "null"))
27
-    p1 <- p1 + theme(plot.margin = unit(c(1, -1, 1.5, 1), "lines"))
25
+    ## p <- p + scale_x_continuous(expand = c(0, 0)) + scale_y_continuous(expand = c(0, 0.6))
26
+    p1 <- p + scale_y_continuous(expand = c(0, 0.6))
27
+    ## p1 <- p + theme(panel.margin=unit(0, "null"))
28
+    ## p1 <- p1 + theme(plot.margin = unit(c(1, -1, 1.5, 1), "lines"))
28 29
     p2 <- gplot.heatmap(p, data, low, high, font.size)
29 30
     grid.arrange(p1, p2, ncol=2, widths=widths)
30 31
     invisible(list(p1=p1, p2=p2))
... ...
@@ -33,8 +34,10 @@ gplot <- function(p, data, low="green", high="red", widths=c(0.5, 0.5), font.siz
33 34
 
34 35
 ##' @importFrom grid unit
35 36
 ##' @importFrom ggplot2 scale_fill_gradient
37
+##' @importFrom ggplot2 scale_fill_discrete
36 38
 ##' @importFrom ggplot2 element_text
37 39
 ##' @importFrom ggplot2 geom_tile
40
+##' @importFrom ggplot2 labs
38 41
 ##' @importFrom reshape2 melt
39 42
 gplot.heatmap <- function(p, data, low, high, font.size) {
40 43
     isTip <- x <- Var1 <- Var2 <- value <- NULL
... ...
@@ -46,25 +49,34 @@ gplot.heatmap <- function(p, data, low, high, font.size) {
46 49
     df=df[df$isTip,]
47 50
     
48 51
     dd$Var1 <- factor(dd$Var1, levels = df$label[order(df$y)])
52
+    if (any(dd$value == "")) {
53
+        dd$value[dd$value == ""] <- NA
54
+    }
49 55
     
50 56
     p2 <- ggplot(dd, aes(Var2, Var1, fill=value))+geom_tile(color="black")
51
-    p2 <- p2 + scale_fill_gradient(low=low, high=high)
57
+    if (is(dd$value,"numeric")) {
58
+        p2 <- p2 + scale_fill_gradient(low=low, high=high, na.value="white")
59
+    } else {
60
+        p2 <- p2 + scale_fill_discrete(na.value="white")
61
+    }
62
+    
52 63
     p2 <- p2+xlab("")+ylab("")
53 64
     p2 <- p2+theme_tree2() + theme(axis.ticks.x = element_blank(),
54 65
                                    axis.line.x=element_blank())
55 66
     ## p1 <- p1 + theme(axis.text.x = element_text(size = font.size))
56 67
     p2 <- p2 + theme(axis.ticks.margin = unit(0, "lines")) 
57 68
     p2 <- p2 + theme(axis.text.x = element_text(size = font.size))
58
-    p2 <- p2 + theme(axis.text.y = element_text(size=font.size))
69
+    ## p2 <- p2 + theme(axis.text.y = element_text(size=font.size))
59 70
     
60 71
     ## plot.margin   margin around entire plot (unit with the sizes of the top, right, bottom, and left margins) 
61 72
     ## units can be given in "lines" or  something more specific like "cm"...
62 73
 
63 74
     
64 75
     p2 <- p2 + theme(panel.margin=unit(0, "null"))
65
-    p2 <- p2 + theme(plot.margin = unit(c(1, 1, 1, -0.5), "lines"))
76
+    p2 <- p2 + theme(plot.margin = unit(c(1, 1, .5, -0.5), "lines"))
66 77
     p2 <- p2 + theme(legend.position = "right")
67
-
78
+    ## p2 <- p2 + labs(fill="")
79
+    
68 80
     return(p2)
69 81
 }
70 82
 
... ...
@@ -159,11 +159,11 @@ setMethod("get.tree", signature(object = "hyphy"),
159 159
 ##' @rdname get.fields-methods
160 160
 ##' @exportMethod get.fields
161 161
 setMethod("get.fields", signature(object = "hyphy"),
162
-          function(object) {
162
+          function(object, ...) {
163 163
               if(length(object@tip_seq) == 0) {
164 164
                   warning("tip sequence not available...\n")
165 165
               } else {
166
-                  object@fields
166
+                  get.fields.tree(object)
167 167
               }
168 168
           })
169 169
 
... ...
@@ -159,7 +159,7 @@ setMethod("get.treetext", signature(object = "jplace"),
159 159
 ##' get.fields(jp)
160 160
 setMethod("get.fields", signature(object = "jplace"),
161 161
           function(object, ...) {
162
-              object@fields
162
+              get.fields.tree(object)
163 163
           }
164 164
           )
165 165
 
166 166
new file mode 100644
... ...
@@ -0,0 +1,119 @@
1
+##' merge two tree object
2
+##'
3
+##' 
4
+##' @title merge_tree
5
+##' @param obj1 tree object 1
6
+##' @param obj2 tree object 2
7
+##' @return tree object
8
+##' @importFrom magrittr %<>%
9
+##' @importFrom ape Ntip
10
+##' @export
11
+##' @author Guangchuang Yu
12
+merge_tree <- function(obj1, obj2) {
13
+    
14
+    if (has.slot(obj1, "extraInfo") == FALSE) {
15
+        stop("input tree object is not supported...")
16
+    }
17
+    
18
+    if ((is.tree(obj1) & is.tree(obj2)) == FALSE) {
19
+        stop("input should be tree objects...")
20
+    }
21
+
22
+    tr1 <- get.tree(obj1)
23
+    tr2 <- get.tree(obj2)
24
+
25
+    if (getNodeNum(tr1) != getNodeNum(tr2)) {
26
+        stop("number of nodes not equals...")
27
+    }
28
+
29
+    if (Ntip(tr1) != Ntip(tr2)) {
30
+        stop("number of tips not equals...")
31
+    }
32
+    
33
+    if (all(tr1$tip.label %in% tr2$tip.label) == FALSE) {
34
+        stop("tip names not match...")
35
+    }
36
+
37
+
38
+    ## order tip.label in tr2 as in tr1
39
+    ## mapping corresponding ID
40
+    idx <- match(tr2$tip.label, tr1$tip.label)
41
+    tr2$edge[match(1:Ntip(tr2), tr2$edge[,2]), 2] <- idx
42
+    tr2$tip.label <- tr1$tip.label
43
+
44
+    node_map <- list()
45
+    node_map$from %<>% c(1:Ntip(tr2))
46
+    node_map$to %<>% c(idx)
47
+
48
+    root <- getRoot(tr1)
49
+    root.2 <- getRoot(tr2)
50
+    tr2$edge[tr2$edge[,1] == root.2, 1] <-  root
51
+
52
+    node_map$from %<>% c(root.2)
53
+    node_map$to %<>% c(root)
54
+
55
+    
56
+    currentNode <- 1:Ntip(tr1)
57
+    while(length(currentNode)) {
58
+        p1 <- sapply(currentNode, getParent, tr=tr1)
59
+        p2 <- sapply(currentNode, getParent, tr=tr2)
60
+
61
+        if (length(p1) != length(p2)) {
62
+            stop("trees are not identical...")
63
+        }
64
+
65
+        jj <- match(p2, tr2$edge[,1])
66
+        if (length(jj)) {
67
+            notNA <- which(!is.na(jj))
68
+            jj <- jj[notNA]
69
+        }
70
+        if (length(jj)) {
71
+            tr2$edge[jj,1] <- p1[notNA]
72
+        }
73
+
74
+        
75
+        ii <- match(p2, tr2$edge[,2])
76
+        if (length(ii)) {
77
+            notNA <- which(!is.na(ii))
78
+            ii <- ii[notNA]
79
+        }
80
+        if (length(ii)) {
81
+            tr2$edge[ii,2] <- p1[notNA]
82
+        }
83
+
84
+        node_map$from %<>% c(p2)
85
+        node_map$to %<>% c(p1)
86
+        
87
+        ## parent of root will return 0, which is in-valid node ID
88
+        currentNode <- unique(p1[p1 != 0])
89
+    }
90
+
91
+    if ( any(tr2$edge != tr2$edge) ) {
92
+        stop("trees are not identical...")
93
+    }
94
+    
95
+    node_map.df <- do.call("cbind", node_map)
96
+    node_map.df <- unique(node_map.df)
97
+    node_map.df <- node_map.df[node_map.df[,1] != 0,]
98
+    i <- order(node_map.df[,1], decreasing = FALSE)
99
+    node_map.df <- node_map.df[i,]
100
+
101
+    info2 <- fortify(obj2)
102
+    info2$node <- node_map.df[info2$node, 2]
103
+    info2$parent <- node_map.df[info2$parent, 2]
104
+
105
+    cn <- colnames(info2)
106
+    i <- match(c("x", "y", "isTip", "label", "branch", "branch.length"), cn)
107
+    i <- i[!is.na(i)]
108
+    info2 <- info2[, -i]
109
+
110
+    extraInfo <- obj1@extraInfo
111
+    if (nrow(extraInfo) == 0) {
112
+        obj1@extraInfo <- info2
113
+    } else {
114
+        info <- merge(extraInfo, info2, by.x =c("node", "parent"), by.y = c("node", "parent"))
115
+        obj1@extraInfo <- info
116
+    }
117
+    
118
+    return(obj1)
119
+}
... ...
@@ -13,7 +13,7 @@
13 13
 ##' read.baseml(rstfile, mlbfile)
14 14
 read.baseml <- function(rstfile, mlbfile) {
15 15
     res <- read.paml_rst(rstfile)
16
-    res@tip_seq <- read.tip_seq_mlb(mlbfile)
16
+    ## res@tip_seq <- read.tip_seq_mlb(mlbfile)
17 17
     set.paml_rst_(res)
18 18
 }
19 19
 
... ...
@@ -24,14 +24,13 @@ read.baseml <- function(rstfile, mlbfile) {
24 24
 ##' @importFrom Biostrings toString
25 25
 ##' @title read.paml_rst
26 26
 ##' @param rstfile rst file
27
-##' @param tip.fasfile fasta file of tips
28 27
 ##' @return A \code{paml_rst} object
29 28
 ##' @export
30 29
 ##' @author Guangchuang Yu \url{http://ygc.name}
31 30
 ##' @examples
32 31
 ##' rstfile <- system.file("extdata/PAML_Baseml", "rst", package="ggtree")
33 32
 ##' read.paml_rst(rstfile)
34
-read.paml_rst <- function(rstfile, tip.fasfile = NULL) {
33
+read.paml_rst <- function(rstfile) {
35 34
     ms <- read.ancseq_paml_rst(rstfile, by="Marginal")
36 35
     phylo <- read.phylo_paml_rst(rstfile)
37 36
     ## class(phylo) <- "list"
... ...
@@ -49,14 +48,16 @@ read.paml_rst <- function(rstfile, tip.fasfile = NULL) {
49 48
                joint_ancseq    = read.ancseq_paml_rst(rstfile, by = "Joint"),
50 49
                rstfile = rstfile
51 50
                )
52
-    if (!is.null(tip.fasfile)) {
53
-        seqs <- readBStringSet(tip.fasfile)
54
-        tip_seq <- sapply(seq_along(seqs), function(i) {
55
-            toString(seqs[i])
56
-        })
57
-        res@tip_seq <- tip_seq
58
-        res@tip.fasfile <- tip.fasfile
59
-    }
51
+    ## if (!is.null(tip.fasfile)) {
52
+    ##     seqs <- readBStringSet(tip.fasfile)
53
+    ##     tip_seq <- sapply(seq_along(seqs), function(i) {
54
+    ##         toString(seqs[i])
55
+    ##     })
56
+    ##     res@tip_seq <- tip_seq
57
+    ##     res@tip.fasfile <- tip.fasfile
58
+    ## }
59
+    res@tip_seq <- ms[names(ms) %in% phylo$tip.label]
60
+    
60 61
     set.paml_rst_(res)
61 62
 }
62 63
 
... ...
@@ -107,12 +108,12 @@ setMethod("get.tipseq", signature(object="paml_rst"),
107 108
 setMethod("show", signature(object = "paml_rst"),
108 109
           function(object) {
109 110
               cat("'paml_rst' S4 object that stored information of\n\t",
110
-                  paste0("'", object@rstfile, "'"))
111
-              if (length(object@tip.fasfile) != 0) {
112
-                  cat(paste0(" and \n\t'", object@tip.fasfile, "'.\n\n"))
113
-              } else {
114
-                  cat(".\n\n")
115
-              }
111
+                  paste0("'", object@rstfile, "'.\n\n"))
112
+              ## if (length(object@tip.fasfile) != 0) {
113
+              ##     cat(paste0(" and \n\t'", object@tip.fasfile, "'.\n\n"))
114
+              ## } else {
115
+              ##     cat(".\n\n")
116
+              ## }
116 117
               cat("...@ tree:")
117 118
               print.phylo(get.tree(object))                  
118 119
               cat("\nwith the following features available:\n")
... ...
@@ -129,7 +130,7 @@ setMethod("get.fields", signature(object = "paml_rst"),
129 130
               if (length(object@tip_seq) == 0) {
130 131
                   warning("tip sequence not available...\n")
131 132
               } else {
132
-                  object@fields
133
+                  get.fields.tree(object)
133 134
               }
134 135
           }
135 136
           )
... ...
@@ -1,15 +1,30 @@
1 1
 
2 2
 ##' @importFrom colorspace rainbow_hcl
3
-scale_color_ <- function(phylo, by, low=NULL, high=NULL, na.color=NULL, default.color="grey") {
3
+scale_color_ <- function(phylo, by, low=NULL, high=NULL, na.color=NULL, default.color="darkgrey", interval=NULL) {
4
+    df <- fortify(phylo)    
5
+    vals <- df[, by]
6
+
7
+    MIN=min(vals, na.rm=TRUE)
8
+    MAX=max(vals, na.rm=TRUE)
9
+
10
+    if (is.null(interval)) {
11
+        interval <- seq(MIN, MAX, length.out=100)
12
+    }
13
+    n <- length(interval)
14
+    
4 15
     if (!is.null(low) & ! is.null(high)) {
5
-        cols <- color_scale(c(low, high))
16
+        cols <- color_scale(low, high, n)
6 17
     } else {
7
-        cols <- rainbow_hcl(100)
18
+        cols <- rainbow_hcl(n)
8 19
     }
9
-    df <- fortify(phylo)
20
+
21
+    ## if (by == "dN_vs_dS") {
22
+    ##     interval <- seq(0, 1.5, length.out = 100)
23
+    ## } 
24
+
25
+    idx <- getIdx(vals, MIN=MIN, MAX=MAX, interval=interval)
26
+    interval <- attr(idx, "interval")
10 27
     
11
-    vals <- df[, by]
12
-    idx <- sapply(vals, getIdx, min(vals, na.rm=TRUE), max(vals, na.rm=TRUE))
13 28
     df$color <- cols[idx]
14 29
 
15 30
     tree <- get.tree(phylo)
... ...
@@ -38,7 +53,10 @@ scale_color_ <- function(phylo, by, low=NULL, high=NULL, na.color=NULL, default.
38 53
     }
39 54
 
40 55
     ## cols[is.na(cols)] <- "grey"
41
-    return(df$color)
56
+    color <- df$color
57
+
58
+    attr(color, "scale") <- list(interval=interval, color=cols)
59
+    return(color)
42 60
 }
43 61
 
44 62
 groupClade_ <- function(object, node) {
... ...
@@ -708,6 +726,27 @@ getYcoord_scale_numeric <- function(tr, df, yscale, ...) {
708 726
     return(df)
709 727
 }
710 728
 
729
+.assign_child_status <- function(tr, df, variable) {
730
+    yy <- df[, variable]
731
+    na.idx <- which(is.na(yy))
732
+    if (length(na.idx) > 0) {
733
+        tree <- get.tree(tr)
734
+        nodes <- rev(getNodes_by_postorder(tree))
735
+        for (curNode in nodes) {
736
+            parent <- getParent(tree, curNode)
737
+            if (parent == 0) { ## already reach root
738
+                next
739
+            }
740
+            idx <- which(is.na(yy[parent]))
741
+            if (length(idx) > 0) {
742
+                yy[parent[idx]] <- yy[curNode]
743
+            }
744
+        }
745
+    }
746
+    df[, variable] <- yy
747
+    return(df)
748
+}
749
+
711 750
 
712 751
 getYcoord_scale_category <- function(tr, df, yscale, yscale_mapping=NULL, ...) {
713 752
     if (is.null(yscale_mapping)) {
... ...
@@ -719,7 +758,10 @@ getYcoord_scale_category <- function(tr, df, yscale, yscale_mapping=NULL, ...) {
719 758
         stop("yscale_mapping should be a named numeric vector...")
720 759
     }
721 760
 
761
+    ## assign to parent status is more prefer...
722 762
     df <- .assign_parent_status(tr, df, yscale)
763
+    df <- .assign_child_status(tr, df, yscale)
764
+    
723 765
     yy <- df[, yscale]
724 766
 
725 767
     ## y <- as.numeric(factor(yy))
... ...
@@ -193,14 +193,15 @@ fortify.beast <- function(model, data,
193 193
     if (time_scale) {
194 194
         df <- scaleX_by_time(df)
195 195
     }
196
-    
197
-    return(df)
196
+
197
+    append_extraInfo(df, model)
198 198
 }
199 199
 
200 200
 scaleX_by_time <- function(df) {
201
-    time <- with(df, gsub(".*_(\\d+\\.*\\d+)$", "\\1", label[isTip])) %>% as.numeric
201
+    time <- with(df, gsub(".*[_/]{1}(\\d+\\.*\\d+)$", "\\1", label[isTip])) %>% as.numeric
202 202
     latest <- which.max(time)
203 203
     df$x <- df$x + time[latest] - max(df$x)
204
+    df$branch <- (df[df$parent, "x"] + df[, "x"])/2
204 205
     return(df)
205 206
 }
206 207
 
... ...
@@ -243,7 +244,8 @@ fortify.codeml <- function(model, data,
243 244
     
244 245
     res <- merge_phylo_anno.codeml_mlc(df, dNdS, ndigits)
245 246
     df <- merge_phylo_anno.paml_rst(res, model@rst)
246
-    scaleY(phylo, df, yscale, layout, ...)
247
+    df <- scaleY(phylo, df, yscale, layout, ...)
248
+    append_extraInfo(df, model)
247 249
 }
248 250
 
249 251
 
... ...
@@ -266,7 +268,8 @@ fortify.codeml_mlc <- function(model, data,
266 268
     dNdS <- model@dNdS
267 269
 
268 270
     df <- merge_phylo_anno.codeml_mlc(df, dNdS, ndigits)
269
-    scaleY(phylo, df, yscale, layout, ...)
271
+    df <- scaleY(phylo, df, yscale, layout, ...)
272
+    append_extraInfo(df, model)
270 273
 }
271 274
 
272 275
 merge_phylo_anno.codeml_mlc <- function(df, dNdS, ndigits = NULL) {
... ...
@@ -320,7 +323,8 @@ fortify.paml_rst <- function(model, data, layout = "phylogram", yscale="none",
320 323
                              ladderize=TRUE, right=FALSE, ...) {
321 324
     df <- fortify.phylo(model@phylo, data, layout, ladderize, right, ...)
322 325
     df <- merge_phylo_anno.paml_rst(df, model)
323
-    scaleY(model@phylo, df, yscale, layout, ...)
326
+    df <- scaleY(model@phylo, df, yscale, layout, ...)
327
+    append_extraInfo(df, model)
324 328
 }
325 329
 
326 330
 merge_phylo_anno.paml_rst <- function(df, model) {
... ...
@@ -349,7 +353,9 @@ fortify.jplace <- function(model, data,
349 353
 
350 354
     df <- df %add2% place
351 355
 
352
-    scaleY(model@phylo, df, yscale, layout, ...)
356
+    df <- scaleY(model@phylo, df, yscale, layout, ...)
357
+
358
+    append_extraInfo(df, model)    
353 359
 }
354 360
 
355 361
 scaleY <- function(phylo, df, yscale, layout, ...) {
... ...
@@ -1,5 +1,66 @@
1
+has.slot <- function(object, slotName) {
2
+    if (!isS4(object)) {
3
+        return(FALSE)
4
+    }
5
+    
6
+    slot <- tryCatch(slot(object, slotName), error=function(e) NULL)
7
+    ! is.null(slot)
8
+}
9
+
10
+has.extraInfo <- function(object) {
11
+    if (!is.tree(object)) {
12
+        return(FALSE)
13
+    }
14
+
15
+    if (! has.slot(object, "extraInfo")) {
16
+        return(FALSE)
17
+    }
18
+
19
+    extraInfo <- object@extraInfo
20
+
21
+    if (nrow(extraInfo) > 0) {
22
+        return(TRUE)
23
+    }
24
+
25
+    return(FALSE)        
26
+}
27
+
28
+append_extraInfo <- function(df, object) {
29
+    if (has.extraInfo(object)) {
30
+        info <- object@extraInfo
31
+        res <- merge(df, info, by.x=c("node", "parent"), by.y=c("node", "parent"))
32
+    } else {
33
+        res <- df
34
+    }
35
+
36
+    i <- order(res$node, decreasing = FALSE)
37
+    res <- res[i,]
38
+    return(res)
39
+}
40
+
41
+get.fields.tree <- function(object) {
42
+    if (is(object, "codeml")) {
43
+        fields <- c(get.fields(object@rst),
44
+                    get.fields(object@mlc))
45
+        fields <- unique(fields)
46
+    } else {
47
+        fields <- object@fields
48
+    }
49
+    
50
+    if (has.slot(object, "extraInfo")) {
51
+        extraInfo <- object@extraInfo
52
+        if (nrow(extraInfo) > 0) {
53
+            cn <- colnames(extraInfo)
54
+            i <- match(c("x", "y", "isTip", "node", "parent", "label", "branch", "branch.length"), cn)
55
+            i <- i[!is.na(i)]
56
+            fields %<>% c(cn[-i])
57
+        }
58
+    }
59
+    return(fields)
60
+}
61
+
1 62
 print_fields <- function(object, len=5) {
2
-    fields <- get.fields(object)
63
+    fields <- get.fields(object)    
3 64
     n <- length(fields)
4 65
     i <- floor(n/len)
5 66
     for (j in 0:i) {
... ...
@@ -60,6 +121,12 @@ get.subs_ <- function(tree, fasta, translate=TRUE, removeGap=TRUE) {
60 121
         if (is.null(res)) {
61 122
             return('')
62 123
         }
124
+        if (nchar(res) > 50) {
125
+            idx <- gregexpr("/", res)[[1]]
126
+            i <- idx[floor(length(idx)/2)]
127
+            res <- paste0(substring(res, 1, i-1), "\n", substring(res, i+1))
128
+        }
129
+        
63 130
         return(res)
64 131
     })
65 132
     
... ...
@@ -209,6 +276,7 @@ is.tree <- function(x) {
209 276
                         "baseml",
210 277
                         "paml_rst",
211 278
                         "baseml_mlc",
279
+                        "codeml",
212 280
                         "hyphy",
213 281
                         "beast")
214 282
         ) {
... ...
@@ -219,21 +287,27 @@ is.tree <- function(x) {
219 287
 
220 288
 
221 289
 
222
-color_scale <- function(c1="grey", c2="red") {
290
+color_scale <- function(c1="grey", c2="red", n=100) {
223 291
     pal <- colorRampPalette(c(c1, c2))
224
-    colors <- pal(100)
292
+    colors <- pal(n)
225 293
     return(colors)
226 294
 }
227 295
 
228
-getIdx <- function(v, MIN, MAX) {
296
+getIdx <- function(v, MIN, MAX, interval=NULL) {
297
+    res <- sapply(v, getIdx_internal, MIN=MIN, MAX=MAX, interval=interval)
298
+    attr(res, "interval") <- interval
299
+    return(res)
300
+}
301
+
302
+getIdx_internal <- function(v, MIN, MAX, interval=NULL) {
229 303
     if (is.na(v)) {
230 304
         return(NA)
231 305
     }
232 306
     if ( MIN == MAX ) {
233 307
         return(100)
234 308
     }
235
-    intervals <- seq(MIN, MAX, length.out=100)
236
-    max(which(intervals <= v))
309
+    res <- max(which(interval <= v))
310
+    return(res)
237 311
 }
238 312
 
239 313
 
240 314
new file mode 100755
... ...
@@ -0,0 +1,77 @@
1
+PB2	PB1	PA	HA	NP	NA	M	NS
2
+A/Swine/Binh_Duong/03_10/2010	trig	trig	trig	HuH3N2	trig	HuH3N2	trig	trig
3
+A/Swine/Binh_Duong/03_08/2010	trig	trig	trig	HuH3N2	trig	HuH3N2	trig	trig
4
+A/Swine/HK/2857/2011	pdm	pdm	pdm	HuH3N2	trig	HuH3N2	pdm	pdm
5
+A/Swine/HK/1071/2012	pdm	pdm	pdm	HuH3N2	trig	HuH3N2	pdm	pdm
6
+A/Swine/HK/2454/2012	pdm	pdm	pdm	HuH3N2	trig	HuH3N2	pdm	pdm
7
+A/Swine/GX_NS2783/2010	pdm	pdm	pdm	HuH3N2	pdm	HuH3N2	pdm	pdm
8
+A/Swine/HK_NS2733/2012	pdm	pdm	pdm	HuH3N2	pdm	HuH3N2	pdm	pdm
9
+A/Swine/HK_NS2439/2011	pdm	pdm	pdm	HuH3N2	pdm	HuH3N2	pdm	pdm
10
+A/Swine/HK/2503/2011	pdm	pdm	pdm	HuH3N2	pdm	HuH3N2	pdm	pdm
11
+A/Swine/GX/2803/2011	pdm	trig	pdm	HuH3N2	pdm	HuH3N2	pdm	pdm
12
+A/Swine/GX_NS3108/2011	pdm	trig	pdm	HuH3N2	pdm	HuH3N2	pdm	pdm
13
+A/Swine/GX_NS3106/2011	pdm	trig	pdm	HuH3N2	pdm	HuH3N2	pdm	pdm
14
+A/Swine/GD/3767/2011	pdm	pdm	pdm	HuH3N2	pdm	HuH3N2	pdm	pdm
15
+A/Swine/GX_NS2394/2012	pdm	pdm	pdm	HuH3N2	pdm	HuH3N2	pdm	pdm
16
+A/Swine/HK_NS2698/2012	pdm	pdm	pdm	HuH3N2	pdm	HuH3N2	pdm	pdm
17
+A/Swine/HK/1284/2012	pdm	pdm	pdm	HuH3N2	pdm	HuH3N2	pdm	pdm
18
+A/Swine/HK/3238/2011	pdm	pdm	pdm	HuH3N2	pdm	HuH3N2	pdm	pdm
19
+A/Swine/HK/459/2012	pdm	pdm	pdm	HuH3N2	pdm	HuH3N2	pdm	pdm
20
+A/Swine/HK_NS2810/2011	pdm	pdm	pdm	HuH3N2	pdm	HuH3N2	pdm	pdm
21
+A/Swine/HK/3700/2011	pdm	pdm	pdm	HuH3N2	pdm	HuH3N2	pdm	pdm
22
+A/Swine/HK/168/2012	pdm	pdm	pdm	HuH3N2	pdm	HuH3N2	pdm	pdm
23
+A/Swine/GD/1599/2012	pdm	pdm	pdm	HuH3N2	pdm	HuH3N2	pdm	pdm
24
+A/Swine/HK_NS1651/2012	pdm	pdm	pdm	HuH3N2	pdm	HuH3N2	pdm	pdm
25
+A/Swine/GD/2919/2012	pdm	pdm	pdm	HuH3N2	pdm	HuH3N2	pdm	pdm
26
+A/Swine/GX/650/2012	pdm	pdm	pdm	HuH3N2	pdm	HuH3N2	pdm	pdm
27
+A/Swine/GX/2242/2011	pdm	pdm	pdm	HuH3N2	pdm	HuH3N2	pdm	pdm
28
+A/Swine/GX/508/2012	pdm	pdm	pdm	HuH3N2	pdm	HuH3N2	pdm	pdm
29
+A/Swine/HK/3280/2012	pdm	pdm	pdm	HuH3N2	pdm	HuH3N2	pdm	pdm
30
+A/Swine/GX_NS1409/2012	pdm	pdm	pdm	HuH3N2	pdm	HuH3N2	pdm	trig
31
+A/Swine/GD_NS2701/2012	pdm	pdm	pdm	HuH3N2	pdm	HuH3N2	pdm	trig
32
+A/Swine/GD_NS2892/2012	pdm	pdm	pdm	HuH3N2	pdm	HuH3N2	pdm	trig
33
+A/Ho_Chi_Minh/459.6/2010				HuH3N2		HuH3N2	pdm	
34
+A/Auckland/615/2002	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2
35
+A/Boston/DOA52/2011	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2
36
+A/Brisbane/09/2006	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2
37
+A/California/NHRC0001/2005	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2
38
+A/California/UR06-0589/2007	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2
39
+A/California/UR07-0017/2008	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2
40
+A/California/VRDL165/2009	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2
41
+A/Colorado/UR06-0023/2007	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2
42
+A/Czech_Republic/119/2012	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2
43
+A/Czech_Republic/126/2012	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2
44
+A/HaNoi/1766/2001	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2
45
+A/HaNoi/BM544/2004	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2
46
+A/Hanoi/BM767/2003	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2
47
+A/Hokkaido/30-1-a/2013				HuH3N2		HuH3N2		
48
+A/Hong_Kong/HKU39/2004	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2
49
+A/Hong_Kong/NHRC0001/2005	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2
50
+A/Kyrgyzstan/WRAIR1255P/2008	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2
51
+A/Malaysia/10816/1999	HuH3N2	HuH3N2		HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2
52
+A/Malaysia/12990/1999	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2
53
+A/Malaysia/29890/2004	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2
54
+A/Malaysia/29997/2004	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2
55
+A/Mexico/InDRE2160/2005	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2
56
+A/Mexico/InDRE29/2006	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2
57
+A/Moscow/328/2003				HuH3N2		HuH3N2	HuH3N2	HuH3N2
58
+A/Moscow/RII05/2012				HuH3N2		HuH3N2	HuH3N2	
59
+A/Netherlands/126/2001	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2
60
+A/Netherlands/42/2006	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2
61
+A/New_York/20342/2010	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2
62
+A/New_York/238/2005	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2
63
+A/New_York/334/2004	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2
64
+A/New_York/435/2000	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2
65
+A/New_York/452/1999	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2
66
+A/New_York/463/2005	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2
67
+A/New_York/523/1998	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2
68
+A/New_York/582/1996	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2
69
+A/New_York/603/1996	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2
70
+A/New_York/657/1994	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2
71
+A/Ohio/UR07-0105/2008	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2
72
+A/Petrozavodsk/RII01/2012				HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2
73
+A/Singapore/H2010.559C/2010	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2
74
+A/South_Carolina/NHRC0001/2006	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2
75
+A/Thailand/CU370/2008	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2
76
+A/Tokyo/Ut-Sk-1/2007	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2
77
+A/Western_Australia/38/2003	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2	HuH3N2
0 78
new file mode 100644
... ...
@@ -0,0 +1,165 @@
1
+#NEXUS
2
+
3
+Begin taxa;
4
+	Dimensions ntax=76;
5
+	Taxlabels
6
+		A/Hokkaido/30-1-a/2013
7
+		A/New_York/334/2004
8
+		A/New_York/463/2005
9
+		A/New_York/452/1999
10
+		A/New_York/238/2005
11
+		A/New_York/523/1998
12
+		A/New_York/435/2000
13
+		A/New_York/582/1996
14
+		A/New_York/603/1996
15
+		A/New_York/657/1994
16
+		A/Western_Australia/38/2003
17
+		A/Auckland/615/2002
18
+		A/Colorado/UR06-0023/2007
19
+		A/California/UR06-0589/2007
20
+		A/Ohio/UR07-0105/2008
21
+		A/Hong_Kong/HKU39/2004
22
+		A/California/UR07-0017/2008
23
+		A/Tokyo/Ut-Sk-1/2007
24
+		A/California/VRDL165/2009
25
+		A/New_York/20342/2010
26
+		A/California/NHRC0001/2005
27
+		A/South_Carolina/NHRC0001/2006
28
+		A/Hong_Kong/NHRC0001/2005
29
+		A/Kyrgyzstan/WRAIR1255P/2008
30
+		A/Mexico/InDRE2160/2005
31
+		A/Mexico/InDRE29/2006
32
+		A/HaNoi/1766/2001
33
+		A/Hanoi/BM767/2003
34
+		A/HaNoi/BM544/2004
35
+		A/Boston/DOA52/2011
36
+		A/Netherlands/126/2001
37
+		A/Netherlands/42/2006
38
+		A/Petrozavodsk/RII01/2012
39
+		A/Malaysia/10816/1999
40
+		A/Malaysia/29997/2004
41
+		A/Malaysia/12990/1999
42
+		A/Malaysia/29890/2004
43
+		A/Brisbane/09/2006
44
+		A/Moscow/328/2003
45
+		A/Thailand/CU370/2008
46
+		A/Singapore/H2010.559C/2010
47
+		A/Czech_Republic/119/2012
48
+		A/Czech_Republic/126/2012
49
+		A/Moscow/RII05/2012
50
+		A/Ho_Chi_Minh/459.6/2010
51
+		A/Swine/Binh_Duong/03_08/2010
52
+		A/Swine/Binh_Duong/03_10/2010
53
+		A/Swine/GX_NS2783/2010
54
+		A/Swine/HK/2503/2011
55
+		A/Swine/HK_NS2439/2011
56
+		A/Swine/GD/3767/2011
57
+		A/Swine/GD/1599/2012
58
+		A/Swine/GX/2242/2011
59
+		A/Swine/GX/2803/2011
60
+		A/Swine/GX_NS3106/2011
61
+		A/Swine/GX_NS3108/2011
62
+		A/Swine/GX/508/2012
63
+		A/Swine/GX/650/2012
64
+		A/Swine/GX_NS1409/2012
65
+		A/Swine/HK_NS2810/2011
66
+		A/Swine/HK/2857/2011
67
+		A/Swine/HK/3238/2011
68
+		A/Swine/HK/3700/2011
69
+		A/Swine/HK/168/2012
70
+		A/Swine/HK/459/2012
71
+		A/Swine/HK/1071/2012
72
+		A/Swine/HK/1284/2012
73
+		A/Swine/HK_NS1651/2012
74
+		A/Swine/HK/2454/2012
75
+		A/Swine/GD_NS2701/2012
76
+		A/Swine/GD_NS2892/2012
77
+		A/Swine/GD/2919/2012
78
+		A/Swine/GX_NS2394/2012
79
+		A/Swine/HK_NS2698/2012
80
+		A/Swine/HK_NS2733/2012
81
+		A/Swine/HK/3280/2012
82
+		;
83
+End;
84
+
85
+Begin trees;
86
+	Translate
87
+		1 A/Hokkaido/30-1-a/2013
88
+		2 A/New_York/334/2004
89
+		3 A/New_York/463/2005
90
+		4 A/New_York/452/1999
91
+		5 A/New_York/238/2005
92
+		6 A/New_York/523/1998
93
+		7 A/New_York/435/2000
94
+		8 A/New_York/582/1996
95
+		9 A/New_York/603/1996
96
+		10 A/New_York/657/1994
97
+		11 A/Western_Australia/38/2003
98
+		12 A/Auckland/615/2002
99
+		13 A/Colorado/UR06-0023/2007
100
+		14 A/California/UR06-0589/2007
101
+		15 A/Ohio/UR07-0105/2008
102
+		16 A/Hong_Kong/HKU39/2004
103
+		17 A/California/UR07-0017/2008
104
+		18 A/Tokyo/Ut-Sk-1/2007
105
+		19 A/California/VRDL165/2009
106
+		20 A/New_York/20342/2010
107
+		21 A/California/NHRC0001/2005
108
+		22 A/South_Carolina/NHRC0001/2006
109
+		23 A/Hong_Kong/NHRC0001/2005
110
+		24 A/Kyrgyzstan/WRAIR1255P/2008
111
+		25 A/Mexico/InDRE2160/2005
112
+		26 A/Mexico/InDRE29/2006
113
+		27 A/HaNoi/1766/2001
114
+		28 A/Hanoi/BM767/2003
115
+		29 A/HaNoi/BM544/2004
116
+		30 A/Boston/DOA52/2011
117
+		31 A/Netherlands/126/2001
118
+		32 A/Netherlands/42/2006
119
+		33 A/Petrozavodsk/RII01/2012
120
+		34 A/Malaysia/10816/1999
121
+		35 A/Malaysia/29997/2004
122
+		36 A/Malaysia/12990/1999
123
+		37 A/Malaysia/29890/2004
124
+		38 A/Brisbane/09/2006
125
+		39 A/Moscow/328/2003
126
+		40 A/Thailand/CU370/2008
127
+		41 A/Singapore/H2010.559C/2010
128
+		42 A/Czech_Republic/119/2012
129
+		43 A/Czech_Republic/126/2012
130
+		44 A/Moscow/RII05/2012
131
+		45 A/Ho_Chi_Minh/459.6/2010
132
+		46 A/Swine/Binh_Duong/03_08/2010
133
+		47 A/Swine/Binh_Duong/03_10/2010
134
+		48 A/Swine/GX_NS2783/2010
135
+		49 A/Swine/HK/2503/2011
136
+		50 A/Swine/HK_NS2439/2011
137
+		51 A/Swine/GD/3767/2011
138
+		52 A/Swine/GD/1599/2012
139
+		53 A/Swine/GX/2242/2011
140
+		54 A/Swine/GX/2803/2011
141
+		55 A/Swine/GX_NS3106/2011
142
+		56 A/Swine/GX_NS3108/2011
143
+		57 A/Swine/GX/508/2012
144
+		58 A/Swine/GX/650/2012
145
+		59 A/Swine/GX_NS1409/2012
146
+		60 A/Swine/HK_NS2810/2011
147
+		61 A/Swine/HK/2857/2011
148
+		62 A/Swine/HK/3238/2011
149
+		63 A/Swine/HK/3700/2011
150
+		64 A/Swine/HK/168/2012
151
+		65 A/Swine/HK/459/2012
152
+		66 A/Swine/HK/1071/2012
153
+		67 A/Swine/HK/1284/2012
154
+		68 A/Swine/HK_NS1651/2012
155
+		69 A/Swine/HK/2454/2012
156
+		70 A/Swine/GD_NS2701/2012
157
+		71 A/Swine/GD_NS2892/2012
158
+		72 A/Swine/GD/2919/2012
159
+		73 A/Swine/GX_NS2394/2012
160
+		74 A/Swine/HK_NS2698/2012
161
+		75 A/Swine/HK_NS2733/2012
162
+		76 A/Swine/HK/3280/2012
163
+		;
164
+tree TREE1 = [&R] 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+A/Swine/Binh_Duong/03_08/2010	6
2
+A/Swine/Binh_Duong/03_10/2010	6
3
+A/Swine/HK/2503/2011	7
4
+A/Swine/HK_NS2439/2011	7
5
+A/Swine/GX_NS2783/2010	7
6
+A/Swine/GD/3767/2011	7
7
+A/Swine/GX/2242/2011	7
8
+A/Swine/GX/2803/2011	7
9
+A/Swine/GX_NS3106/2011	7
10
+A/Swine/GX_NS3108/2011	7
11
+A/Swine/HK_NS2810/2011	7
12
+A/Swine/HK/2857/2011	7
13
+A/Swine/HK/3238/2011	7
14
+A/Swine/HK/3700/2011	7
15
+A/Swine/HK/168/2012	7
16
+A/Swine/HK/459/2012	7
17
+A/Swine/HK/1071/2012	7
18
+A/Swine/HK/1284/2012	7
19
+A/Swine/GX/650/2012	7
20
+A/Swine/GX_NS1409/2012	8
21
+A/Swine/GD/1599/2012	6
22
+A/Swine/HK/2454/2012	7
23
+A/Swine/GX/508/2012	7
24
+A/Swine/HK_NS1651/2012	7
25
+A/Swine/HK_NS2733/2012	7
26
+A/Swine/HK/3280/2012	7
27
+A/Swine/GX_NS2394/2012	7
28
+A/Swine/GD_NS2701/2012	8
29
+A/Swine/GD_NS2892/2012	8
30
+A/Swine/GD/2919/2012	6
31
+A/Swine/HK_NS2698/2012	8
32
+A/Ho_Chi_Minh/459.6/2010	7
33
+A/Netherlands/42/2006	10
34
+A/Malaysia/29890/2004	11
35
+A/New_York/334/2004	11
36
+A/New_York/463/2005	11
37
+A/New_York/238/2005	11
38
+A/HaNoi/BM544/2004	10
39
+A/Hong_Kong/HKU39/2004	11
40
+A/Malaysia/29997/2004	10
41
+A/Western_Australia/38/2003	10
42
+A/Moscow/328/2003	11
43
+A/Hanoi/BM767/2003	12
44
+A/California/UR06-0589/2007	11
45
+A/Brisbane/09/2006	11
46
+A/Tokyo/Ut-Sk-1/2007	9
47
+A/South_Carolina/NHRC0001/2006	11
48
+A/Mexico/InDRE2160/2005	11
49
+A/Colorado/UR06-0023/2007	11
50
+A/Hong_Kong/NHRC0001/2005	11
51
+A/California/NHRC0001/2005	11
52
+A/Mexico/InDRE29/2006	11
53
+A/California/VRDL165/2009	10
54
+A/California/UR07-0017/2008	11
55
+A/Ohio/UR07-0105/2008	10
56
+A/Kyrgyzstan/WRAIR1255P/2008	11
57
+A/Thailand/CU370/2008	11
58
+A/Moscow/RII05/2012	11
59
+A/Hokkaido/30-1-a/2013	12
60
+A/Czech_Republic/119/2012	11
61
+A/Petrozavodsk/RII01/2012	11
62
+A/New_York/20342/2010	11
63
+A/Boston/DOA52/2011	11
64
+A/Czech_Republic/126/2012	11
65
+A/Singapore/H2010.559C/2010	11
66
+A/Auckland/615/2002	10
67
+A/New_York/657/1994	9
68
+A/Malaysia/12990/1999	11
69
+A/HaNoi/1766/2001	11
70
+A/Malaysia/10816/1999	11
71
+A/Netherlands/126/2001	11
72
+A/New_York/435/2000	11
73
+A/New_York/452/1999	10
74
+A/New_York/523/1998	10
75
+A/New_York/582/1996	9
76
+A/New_York/603/1996	9
0 77
new file mode 100644
... ...
@@ -0,0 +1,1350 @@
1
+
2
+Before deleting alignment gaps
3
+     76   1698
4
+
5
+A/Swine/Binh_Duong/03_08/2010  ATG AAG ACT ATC ATT GCT TTG AGC TAC ATT CTA TGT CTG GTT TTC GCT CAA AAA TTT CCT GGA AAT GAC AAC AGC ATG GCA ACG CTG TGC CTT GGG CAC CAT GCA GTA CCA AAC GGA ACG ATG GTG AAA ACA ATC ACG AAT GAC CAA ATT GAA GTT ACT AAT GCT ACT GAG CTG GTT CAG AGT TCC TCA ACA GGT GGA ATA TGC AAC AGC CCT CAT CAG ATC CTT GAT GGA GGA AAC TGC ACA CTA ATA GAT GCT CTA TTG GGA GAC CCT CAG TGT GAT GGC TTC CAA AAT AAG AAA TGG GAC CTT TTT GTT GAA CGC AGC AAA GCC TAC AGC AAC TGT TAC CCT TAT GAT GTA CCG GAT TAT GCC TCC CTT AGG TCA ATA GTT GCC TCA TCC GGC ACA CTA GAA TTT AAC AGT GAA AAC TTC AAT TGG ACT GGA GTC ACT CAA AAT GGA AAA AGC TCT TCT TGC AAA AGG GGA TCT GAT AGC AGT TTC TTT AGT AGA TTG AAT TGG TTG ACC CAC TTA AAT TAC AAA TAT CCA GCA TTG AAA GTT ACT ATG CCA AAC AAT GAA AAA TTT GAC AAA TTG TAC ATT TGG GGG GTT CAC CAC CCG GGT ACG TAC AAT GAC CAA ATC AGC CTA TAT GCT CAA GCA TCA GGA ATA ATC ACA GTC TCT ACC AAA AGA AAC CAA CAA ACT GTG ATC CCG AAT ATC GGA TCT AGA CCC AGA GTA AGG GAT ATC CCC AGC AGA ATA AGC ATC TAT TGG ACA ATA GTA AAA CCT GGA GAC ATA CTT TTG ATT AAC AGC ACA GGG AAT CTA ATT CCT CCT CGG GGT TAC TTC AAA ATA CAA AGT GGG AGA AGC TCA ATA ATG AGG TCA GAT GCA CCC ATT GGC AAA TGC AAT TCC GAA TGT ATC ACT CCA AAT GGA AGC ATT CCC AAT GAC AAA CCA TTT CAA AAT GTA AAC AGG ATC ACC TAT GGG GCC TGT CCC AGA TAT GTT AAG CAA AAC ACT CTG AAA TTG GCA ACA GGG ATG AGA AAT GTA CCA GAG AAA CAA ACT AGA GGC ATA TTT GGC GCA ATC GCG GGT TTC ATA GAA AAT GGT TGG GAG GGA ATG GTG GAT GGT TGG TAC GGT TTC AGG CAT AAA AAT TCT GAG GGA ATG GGA CAA GCA GCA GAT CTC AAA AGC ACT CAA GCA GCA ATT AAC CAA ATC AAT GGA AAG CTG AAT AGG TTG ATC GGG AAA ACC AAT GAG AAA TTC CAT CAG ATT GAA AAA GAA TTC TCA GAG GTA GAA GGG AGA ATT CAG GAC CTC GAG AAA TAT GTT GAG GAC ACC AAA ATA GAT CTC TGG TCA TAC AAT GCG GAG CTT CTT GTT GCC CTG GAG AAC CAA CAT ACA ATT GAT CTA ACT GAC TCA GAA ATG AAC AAA CTG TTT GAA AGA ACA AAG AAG CAA CTG AGG GAA AAT GCT GAG GAT ATG GGC AAT GGT TGT TTC AAA ATA TAC CAC AAA TGT GAC AAT GCC TGC ATA GGA TCA ATC AGA AAT GGA ACT TAT GAC CAT GAT ATA TAC AGA GAT GAA GCA TTG AAC AAC CGG TTC CAG ATC AAA GGT GTT GAG CTG AAG GCA GGA TAC AAA GAT TGG ATC CTA TGG ATT TCC TTT GCC ATA TCA TGT TTT TTG CTT TGT GTT GTT TTG TTG GGG TTC ATC ATG TGG GCC TGC CAA AAA GGC AAC ATT AGG TGC AAC ATT TGC ATT 
6
+A/Swine/Binh_Duong/03_10/2010  ATG AAG ACT ATC ATT GCT TTG AGC TAC ATT CTA TGT CTG GTT TTC GCT CAA AAA TTT CCT GGA AAT GAC AAC AGC ATG GCA ACG CTG TGC CTT GGG CAC CAT GCA GTA CCA AAC GGA ACG ATG GTG AAA ACA ATC ACG AAT GAC CAA ATT GAA GTT ACT AAT GCT ACT GAG CTG GTT CAG AGT TCC TCA ACA GGT GGA ATA TGC AAC AGC CCT CAT CAG ATC CTT GAT GGA GGA AAC TGC ACA CTA ATA GAT GCT CTA TTG GGA GAC CCT CAG TGT GAT GGC TTC CAA AAT AAG AAA TGG GAC CTT TTT GTT GAA CGC AGC AAA GCC TAC AGC AAC TGT TAC CCT TAT GAT GTA CCG GAT TAT GCC TCC CTT AGG TCA ATA GTT GCC TCA TCC GGC ACA CTA GAA TTT AAC AGT GAA AAC TTC AAT TGG ACT GGA GTC ACT CAA AAT GGA AAA AGC TCT TCT TGC AAA AGG GGA TCT GAT AGC AGT TTC TTT AGT AGA TTG AAT TGG TTG ACC CAC TTA AAT TAC AAA TAT CCA GCA TTG AAA GTT ACT ATG CCA AAC AAT GAA AAA TTT GAC AAA TTG TAC ATT TGG GGG GTT CAC CAC CCG GGT ACG TAC AAT GAC CAA ATC AGC CTA TAT GCT CAA GCA TCA GGA ATA ATC ACA GTC TCT ACC AAA AGA AAC CAA CAA ACT GTG ATC CCG AAT ATC GGA TCT AGA CCC AGG GTA AGG GAT ATC CCC AGC AGA ATA AGC ATC TAT TGG ACA ATA GTA AAA CCT GGA GAC ATA CTT TTG ATT AAC AGC ACA GGG AAT CTA ATT GCT CCT CGG GGT TAC TTC AAA ATA CAA AGT GGG AGA AGC TCA ATA ATG AGG TCA GAT GCA CCC ATT GGC AAA TGC AAT TCC GAA TGT ATC ACT CCA AAT GGA AGC ATT CCC AAT GAC AAA CCA TTT CAA AAT GTA AAC AGG ATC ACC TAT GGG GCC TGT CCC AGA TAT GTT AAG CAA AAC ACT CTG AAA TTG GCA ACA GGG ATG AGA AAT GTA CCA GAG AAA CAA ACT AGA GGC ATA TTT GGC GCA ATC GCG GGT TTC ATA GAA AAT GGT TGG GAG GGA ATG GTG GAT GGT TGG TAC GGT TTC AGG CAT AAA AAT TCT GAG GGA ATG GGA CAA GCA GCA GAT CTC AAA AGC ACT CAA GCA GCA ATT AAC CAA ATC AAT GGA AAG CTG AAT AGG TTG ATC GGG AAA ACC AAT GAG AAA TTC CAT CAG ATT GAA AAA GAA TTC TCA GAG GTA GAA GGG AGA ATT CAG GAC CTC GAG AAA TAT GTT GAG GAC ACC AAA ATA GAT CTC TGG TCA TAC AAT GCG GAG CTT CTT GTT GCC CTG GAG AAC CAA CAT ACA ATT GAT CTA ACT GAC TCA GAA ATG AAC AAA CTG TTT GAA AGA ACA AAG AAG CAA CTG AGG GAA AAT GCT GAG GAT ATG GGC AAT GGT TGT TTC AAA ATA TAC CAC AAA TGT GAC AAT GCC TGC ATA GGA TCA ATC AGA AAT GGA ACT TAT GAC CAT GAT ATA TAC AGA GAT GAA GCA TTG AAC AAC CGG TTC CAG ATC AAA GGT GTT GAG CTG AAG GCA GGA TAC AAA GAT TGG ATC CTA TGG ATT TCC TTT GCC ATA TCA TGT TTT TTG CTT TGT GTT GTT TTG TTG GGG TTC ATC ATG TGG GCC TGC CAA AAA GGC AAC ATT AGG TGC AAC ATT TGC ATT 
7
+A/Swine/HK/2503/2011       ATG AAG ACT ATC ATT GCT TTG AGC TAC ATT CTA TGT CTG GTT TTC GCT CAA AAA TTT CCT GGA AAT GAC AAC AGC ATG GCA ACG CTG TGC CTT GGG CAC CAT GCA GTA CCA AAC GGA ACG ATG GTG AAA ACA ATC ACG AAT GAC CAA ATT GAA GTT ACT AAT GCT ACT GAG CTG GTT CAG AGT TCC TCA ACA GGT GGA ATA TGC AAC AGC CCT TAT CAG ATC CTT GAT GGA GGA AAC TGC ACA CTA ATA GAT GCT CTA TTG GGA GAC CCT CAG TGT GAT GGC TTC CAG AAT AAG AAA TGG GAC CTT TTT ATT GAA CGC AGC AAA GCC TAC AGC AAC TGT TAC CCT TAT GAT GTG CCG GAT TAT TCC TCC CTT AGG TCA ATA GTT GCC TCA TCC GGC ACG CTG GAA TTT AAC AAT GAA AGC TTC AAT TGG ACT GGA GTA ACT CAA AAT GGA AAA AGC GCT TCT TGC AAA AGG GGA TCT GAT AAC AGT TTC TTT AGT AGA TTG AAT TGG TTG ACC CAC TTA AAT TAC AAA TAT CCA GCA TTG AAA GTT ACT ATG CCA AAC AAT GAA AAA TTT GAC AAA TTG TAC ATT TGG GGG GCT CAC CAC CCG AGT ACG TAC AGT GAC CAA ATC AGC CTA TAT GCT CAA GCA TCA GGA ATA ATC ACA GTC TCT ACC AAA AGA ACC CAA CAA ACT GTG ATC CCG AAT ATC GGA TCT AGA CCC AGA GTA AGG GAT ATC CCC AGC AGA ATA AGC ATC TAT TGG ACA ATA GTA AAA CCG GGA GAC ATA CTT TTG ATT AAC AGC ACA GGG AAT CTA ATT GCT CCT CGG GGT TAT TTC AAA ATA CAA AGT GGG AAA AGC TCA ATA ATG AGA TCA GAT GCA CCC ATT GGC AAA TGC AAT TCT GAA TGT ATC ACT CCA AAT GGA AGC ATT CCC AAT GAC AAA CCA TTT CAA AAT GTA AAT AGG ATC ACA TAT GGG GCC TGT CCC AGA TAT GTT AAG CAA AAC ACC CTG AAA TTG GCA ACA GGA ATG AGA AAT GTA CCA GAG AAA CAA ACT AGA GGC ATA TTT GGC GCA ATC GCA GGT TTC ATA GAA AAT GGT TGG GAG GGA ATG GTT GAT GGT TGG TAC GGT TTC AGG CAT CAA AAT TCT GAG GGA ATG GGA CAA GCA GCA GAT CTC AAA AGC ACT CAA GCA GCA ATC AAT CAA ATC AAT GGA AAG CTG AAT AGG TTG ATC GGG AAA ACC AAT GAG AAA TTC CAT CAG ATT GAA AAA GAA TTC TCA GAG GTA GAA GGG AGA ATT CAG GAC CTC GAG AAA TAT GTT GAG GAC ACC AAA ATA GAT CTC TGG TCA TAC AAC GCG GAA CTT CTT GTT GCC CTG GAG AAC CAA CAT ACA ATT GAT CTA ACT GAC TCA GAA ATG AAC AAA CTG TTT GAA AGA ACA AAG AAG CAA CTG AGG GAA AAT GCT GAG GAT ATG GGC AAT GGT TGT TTC AAA ATA TAC CAC AAA TGT GAC AAT GCC TGC ATA GGA TCA ATC AGA AAT GGA ACT TAT GAC CAT GAT GTA TAC AGA GAT GAA GCA TTG AAC AAC CGG TTC CAG ATC AAA GGT GTT GAG CTG AAG GCA GGA TAC AAA GAT TGG ATC CTA TGG ATT TCC TTT GCC ATA TCA TGT TTT TTG CTT TGT GTT GTT TTG TTG GGG TTC ATC ATG TGG GCC TGC CAA AAG GGC AAC ATT AGG TGC AAC ATT TGC ATT 
8
+A/Swine/HK_NS2439/2011     ATG AAG ACT ATC ATT GCT TTG AGC TAC ATT CTA TGT CTG GTT TTC GCT CAA AAA TTT CCT GGA AAT GAC AAC AGC ATG GCA ACG CTG TGC CTT GGG CAC CAT GCA GTA CCA AAC GGA ACG ATG GTG AAA ACA ATC ACG AAT GAC CAA ATT GAA GTT ACT AAT GCT ACT GAG CTG GTT CAG AGT TCC TCT ACA GGT GGA ATA TGC AAC AGC CCT TAT CAG ATC CTT GAT GGA GGA AAC TGC ACA CTA ATA GAT GCT CTA TTG GGA GAC CCT CAG TGT GAT GGC TTC CAG AAT AAG AAA TGG GAC CTT TTT GTT GAA CGC AGC AAA GCC CAC AGC AAC TGC TAC CCT TAT GAT GTG CCG GAT TAT GCC TCC CTT AGG TCA ATA GTT GCC TCA TCC GGC ACG CTG GAA TTT AAC AAT GAA AGC TTC AAT TGG ACT GGA GTC ACT CAA AAT GGA AAA AGC GCT TCT TGC AAA AGG GGA TCT GAT AAC AGT TTC TTT AGT AGA TTG AAT TGG TTG ACC CAC TTA AAT TAC AAA TAT CCA GCA TTG AAA GTT ACT ATG CCA AAC AAT GAA AAA TTT GAC AAA TTG TAC ATT TGG GGG GCT CAC CAC CCG AGT ACG TAC AGT GAC CAA ATC AGC CTA TAT GCT CAA GCA TCA GGA ATA ATC ACA GTC TCT ACC AAA AGA ACC CAA CAA ACT GTG ATC CCG AAT ATC GGA TCT AGA CCC AGA GTA AGG GAT ATC CCC AGC AGA ATA AGC ATC TAT TGG ACA ATA GTA AAA CCG GGA GAC ATA CTT TTG ATT AAC AGC ACA GGG AAT TTA ATT GCT CCT CGA GGT TAT TTC AAA ATA CAA AGT GGG AAA AGC TCA ATA ATG ATA TCA GAT GCA CCC ATT GGC AAA TGC AAT TCT GAA TGT ATC ACT CCA AAT GGA AGC ATT CCC AAT GAC AAA CCA TTT CAA AAT GTA AAT AGG ATC ACA TAT GGG GCC TGT CCC AGA TAT GTT AAG CAA AAC ACC CTG AAA TTG GCA ACA GGA ATG AGA AAT GTA CCA GAG AAA CAA ACT AGA GGC ATA TTT GGC GCA ATC GCG GGT TTC ATA GAA AAT GGT TGG GAG GGA ATG GTT GAT GGT TGG TAC GGT TTC AGG CAT CAA AAT TCT GAG GGA ATG GGA CAA GCA GCA GAT CTC AAA AGC ACT CAA GCA GCA ATC AAT CAA ATC AAT GGA AAG CTG AAT AGG TTG ATC GGG AAA ACC AAT GAG AAA TTC CAT CAG ATT GAA AAA GAA TTC TCA GAG GTA GAA GGG AGA ATT CAG GAC CTC GAG AAA TAT GTT GAG GAC ACC AAA ATA GAT CTC TGG TCA TAC AAC GCG GAA CTT CTT GTT GCC CTG GAG AAC CAA CAT ACA ATT GAT CTA ACT GAC TCA GAA ATG AAC AAA CTG TTT GAA AGA ACA AAG AAG CAA CTG AGG GAA AAT GCT GAG GAT ATG GGC AAT GGT TGT TTC AAA ATA TAC CAC AAA TGT GAC AAT GCC TGC ATA GGA TCA ATC AGA AAT GGA ACT TAT GAC CAT GAT GTA TAC AGA GAT GAA GCA TTG AAC AAC CGG TTC CAG ATC AAA GGT GTT GAG CTG AAG GCA GGA TAC AAA GAT TGG ATC CTA TGG ATT TCC TTT GCC ATA TCA TGT TTT TTG CTT TGT GTT GTT TTG TTG GGG TTC ATC ATG TGG GCC TGC CAA AAG GGC AAC ATT AGG TGC AAC ATT TGC ATT 
9
+A/Swine/GX_NS2783/2010     ATG AAG ACT ATC ATT GCT TTG AGC TAC ATT CTA TGT CTG GTT TTC GCT CAA AAA TTT CCT GGA AAT GAC AAC AGC ATG GCA ACG CTG TGC CTT GGG CAC CAT GCA GTA CCA AAC GGA ACG ATG GTG AAA ACA ATC ACG AAT GAC CAA ATT GAA GTT ACT AAT GCT ACT GAG CTG GTT CAG AGT TCC TCA ACA GGT GGA ATA TGC AAC AGC CCT TAT CAG ATC CTT GAT GGA GGA AAC TGC ACA CTA ATA GAT GCT CTA TTG GGA GAC CCT CAG TGT GAT GGC TTC CAG AAT AAG AAA TGG GAC CTT TTT GTT GAA CGC AGC AAA GCC TAC AGC AAC TGT TAC CCT TAT GAT ATG CCG GAT TAT GCC TCC CTT AGG TCA ATA GTT GCC TCA TCC GGC ACG CTG GAA TTT AAC AAT GAA AGC TTC AAT TGG ACT GGA GTC ACT CAA AAT GGA AAA AGC GCT TCT TGC AAA AGG GGA TCT GAT AAC AGT TTC TTT AGT AGA TTG AAT TGG TTG ACC CAC TTA AAT TAC AAA TAT CCA GCA TTG AAA GTT ACT ATG CCA AAC AAT GAA AAA TTT GAC AAA TTG TAC ATT TGG GGG GCT CAC CAC CCG AGT ACG TAC AAT GAC CAA ATC AGC CTA TAT GCT CAA GCA TCA GGA ATA ATC ACA GTC TCT ACC AAA AGA ACC CAA CAA ACT GTG ATC CCG AAT ATC GGA TCT AGA CCC AGA GTA AGG GAT ATC CCC AGC AGA ATA AGC ATC TAT TGG ACA ATA GTA AAA CCG GGA GAC ATA CTT TTG ATT AAC AGC ACA GGG AAT CTA ATT GCT CCT CGG GGT TAT TTC AAA ATA CAA AGT GGG AAA AGC TCA ATA ATG AGA TCA GAT GCA CCC ATT GGC AAA TGC AAT TCT GAA TGT ATC ACT CCA AAT GGA AGC ATT CCC AAT GAC AAA CCA TTT CAA AAT GTA AAT AGG ATC ACA TAT GGG GCC TGT CCC AGA TAT GTT AAG CAA AAC ACC CTG AAA TTG GCA ACA GGA ATG AGA AAT GTA CCA GAG AAA CAA ACT AGA GGC ATA TTT GGC GCA ATC GCG GGT TTC ATA GAA AAT GGT TGG GAG GGA ATG GTT GAT GGT TGG TAC GGT TTC AGG CAT CAA AAT TCT GAG GGA ATG GGA CAA GCA GCA GAT CTC AAA AGC ACT CAA GCA GCA ATC AAT CAA ATC AAT GGA AAG CTG AAT AGG TTG ATC GGG AAA ACC AAT GAG AAA TTC CAT CAG ATT GAA AAA GAA TTC TCA GAG GTA GAA GGG AGA ATT CAG GAC CTC GAG AAA TAT GTT GAG GAC ACC AAA ATA GAT CTC TGG TCA TAC AAC GCG GAA CTT CTT GTT GCC CTG GAG AAC CAA CAT ACA ATT GAT CTA ACT GAC TCA GAA ATG AAC AAA CTG TTT GAA AGA ACA AAG AAG CAA CTG AGG GAA AAT GCT GAG GAT ATG GGC AAT GGT TGT TTC AAA ATA TAC CAC AAA TGT GAC AAT GCC TGC ATA GGA TCA ATC AGA AAT GGA ACT TAT GAC CAT GAT GTA TAC AGA GAT GAA GCA TTG AGC AAC CGG TTC CAG ATC AAA GGT GTT GAG CTG AAG GCA GGA TAC AAA GAT TGG ATC CTA TGG ATT TCC TTT GCC ATA TCA TGT TTT TTG CTT TGT GTT GTT TTG TTG GGG TTC ATC ATG TGG GCC TGC CAA AAG GGC AAC ATT AGG TGC AAC ATT TGC ATT 
10
+A/Swine/GD/3767/2011       ATG AAG ACT ATC ATT GCT TTG AGC TAC ATT CTA TGT CTG GTT TTC GCT CAA AAA TTT CCT GGA AAT GAC AAC AAC ATG GCA ATG CTG TGC CTT GGG CAC CAT GCA GTA CCA AAC GGA ACG ATG GTG AAA ACA ATC ACG AAT GAC CAA ATT GAA GTT ACT AAT GCT ACT GAG CTG GTT CAG AGT TCC TCA ACA GGT GGA ATA TGC AAC AGC CCT TAT CAG ATC CTT GAT GGA GGA AAC TGC ACA CTA ATA GAT GCT CTA TTG GGA GAC CCT CAG TGT GAT GGC TTC CAG AAT AAG AAA TGG GAC CTT TTT GTT GAA CGC AGC AAA GCC TAC AGC AAT TGT TAC CCT TAT GAT GTG CCG GAT TAT GCC TCC CTT AGG TCA ATA GTT GCC TCA TCC GGC ACG CTG GAA TTT AAC AAT GAA AGC TTC AAT TGG ACT GGA GTC ACT CAA AAT GGA AAA AGC GCT TCT TGC AAA AGG GGA TCT GAT AAC AGT TTC TTT AGT AGA TTG AAT TGG TTG ACC CAC TTA AAT TAC AAA TAT CCA GCA TTG AAA GTT ACT ATG CCA AAC AAT GAA AAA TTT GAC AAA TTG TAC ATT TGG GGG GCT CAC CAC CCG GGT ACG TAC AAT GAC CAA ATC AGC CTA TAT GCT CAA GCA TCA GGA ATA ATC ACA GTC TCT ACC AAA AGA ACC CAA CAA ACT GTG ATC CCG AAT ATC GGA TCT AGA CCC AGA GTA AGG GAT ATC CCC AGC AGA ATA AGC ATC TAT TGG ACA ATA GTA AAA CCG GGA GAC ATA CTT TTG ATT AAC AGC ACA GGG AAC CTA ATT GCT CCT CGG GGT TAT TTC AAA CTA CAA AAT GAG AAA AGC TCA ATA ATG AGA TCA GAT GCA CCC ATT GGC AAA TGC AAT TCT GAA TGT ATC ACC CCA AAT GGA AGC ATT CCC AAT GAC AGA CCA TTT CAA AAT GTA AAT AGG ATC ACA TAT GGG GCC TGT CCC AGA TAT GTT AAG CAA AAC ACC CTG AAA TTG GCA ACA GGA ATG AGA AAT GTA CCA GAG AAA CAA ACT AGA GGC ATA TTT GGC GCA ATT GCG GGT TTC ATA GAA AAT GGT TGG GAG GGA ATG GTT GAT GGT TGG TAC GGT TTC AGG CAC CAA AAT TCT GAG GGA ATG GGA CAA GCA GCA GAT CTC AAA AGC ACT CAA GCA GCA ATC AAT CAA ATC AAT GGA AAG CTG AAT AGG TTG ATC GGG AAA ACC AAT GAG AAA TTC CAT CAG ATT GAA AAA GAG TTC TCA GAG GTA GAA GGA AGA ATT CAG GAC CTC GAG AAA TAT GTT GAG GAC ACC AAA ATA GAT CTC TGG TCA TAC AAC GCG GAG CTT CTT GTT GCC CTG GAG AAC CAA CAT ACA ATT GAT CTA ACT GAC TCA GAA ATG AAC AAA CTG TTT GAA AGA ACA AAG AAG CAA CTG AGG GAA AAT GCT GAG GAT ATG GGC AAT GGT TGT TTC AAA ATA TAC CAC AAG TGT GAC AAT GCC TGC ATA GGA TCA ATC AGA AAT GGA ACT TAT GAC CAT GAT GTA TAC AGA GAT GAA GCA TTG AGC AAC CGG TTC CAG ATC AAA GGT GTT GAG CTG AAG GCA GGA TAC AAA GAT TGG ATC CTA TGG ATT TCC TTT GCC ATA TCA TGT TTT TTG CTT TGT GTT GTT CTG TTG GGG TTC ATC ATG TGG GCC TGC CAA AAG GGC AAC ATT AGG TGC AAC ATT TGC ATT 
11
+A/Swine/GX/2242/2011       ATG AAG ACT ATC ATT GCT TTG AGC TAC ATT CTA TGT CTG GTT TTC GCT CAA AAA TTT CCT GGA AAT GAC AAC AAC ATG GCA ATG CTG TGC CTT GGG CAC CAT GCA GTA CCA AAC GGA ACG ATG GTG AAA ACA ATC ACA AAT GAC CAA ATT GAA GTT ACT AAT GCT ACT GAG CTG GTT CAG AGT TCC TCA ACA GGT GGA ATA TGC AAC AGC CCT TAT CAG ATC CTT GAT GGA GGA AAC TGC ACA CTA ATA GAT GCT CTA TTG GGA GAC CCT CAG TGT GAT GGC TTC CAG AAT AAG AAA TGG GAC CTT TTT GTT GAA CGC AGC AAA GCC TAC AGC AAC TGT TAC CCT TAT GAT GTG CCG GAT TAT GCC TCC CTT AGG TCA ATA GTT GCC TCA TCC GGC ACG CTG GAA TTT AAC AAT GAA AGC TTC AAT TGG ACT GGA GTC ACT CAA AAT GGA AAA AGC GCT TCT TGC AAA AGG GGA TCT GAT AAC AGT TTC TTT AGT AGA TTG AAT TGG TTG ACC CAC TTA AAT TAC AAA TAT CCA GCA TTG AAA GTT ACT ATG CCA AAC AAT GAA AAA TTT GAC AAA TTG TAC ATT TGG GGG GCT CAC CAC CCG GGT ACG TAC AAT GAC CAA ATC AGC CTA TAT GCT CAA GCA TCA GGA ATA ATC ACA GTC TCT ACC AAA AGA ACC CAA CAA ACT GTG ATC CCG AAT ATC GGA TCT AGA CCC AGA GTA AGG GAT ATC CCC AGC AGA ATA AGC ATC TAT TGG ACA ATA GTA AAA CCG GGA GAC ATA CTT TTG ATT AAC AGC ACA GGG AAT CTA ATT GCT CCT CGG GGT TAT TTC AAA TTA CAA AAT GGG AAA AGC TCA ATA ATG AGA TCA GAT GCA CCC ATT GGC AAA TGC AAT TCT GAA TGT ATC ACC CCA AAT GGA AGC ATT CCC AAT GAC AGA CCA TTT CAA AAT GTA AAT AGG ATC ACA TAT GGG ACC TGT CCC AGA TAT GTT AAG CAA AAC ACC CTG AAA TTG GCA ACA GGA ATG AGA AAT GTA CCA GAG AAA CAA ACT AGA GGC ATA TTT GGC GCA ATC GCG GGT TTC ATA GAA AAT GGT TGG GAG GGA ATG GTT GAT GGT TGG TAC GGT TTC AGG CAC CAA AAT TCT GAG GGA ATG GGA CAA GCA GCA GAT CTC AAA AGC ACT CAA GCA GCA ATT AAT CAA ATC AAT GGA AAG CTG AAT AGG TTG ATC GGG AAA ACC AAT GAG AAA TTC CAT CAG ATT GAA AAA GAA TTC TCA GAG GTA GAA GGA AGA ATT CAG GAC CTC GAG AAA TAT GTT GAG GAC ACC AAA ATA GAT CTC TGG TCA TAC AAC GCG GAG CTT CTT GTT GCC CTG GAG AAC CAA CAT ACA ATT GAT CTA ACT GAC TCA GAA ATG AAC AAA CTG TTT GAA AGA ACA AAG AAG CAA CTG AGG GAA AAT GCT GAG GAT ATG GGC AAT GGT TGT TTC AAA ATA TAC CAC AAA TGT GAC AAT GCC TGC ATA GGA TCA ATC AGA AAT GGA ACT TAT GAC CAT GAT GTA TAC AGA GAT GAA GCA TTG AGC AAC CGG TTC CAG ATC AAA GGT GTT GAG CTG AAG GCA GGA TAC AAA GAT TGG ATC CTA TGG ATT TCC TTT GCC ACA TCA TGT TTT TTG CTT TGT GTT GTT TTG TTG GGG TTC ATC ATG TGG GCC TGC CAA AAG GGC AAC ATT AGG TGC AAC ATT TGC ATT 
12
+A/Swine/GX/2803/2011       ATG AAG ACT ATC ATT GCT TTG AGC TAC ATT CTA TGT CTG GTT TTC GCT CAA AAA TTT CCT GGA AAT GAC AAC AGC ATG GCA ACG CTG TGC CTT GGG CAC CAT GCA GTA CCA AAC GGA ACG ATG GTG AAA ACA ATC ACG AAT GAC CAA ATT GAA GTT ACT AAT GCT ACT GAG CTG GTT CAG AGT TCC TCA ACA GGT GGA CTA TGC AAC AGC CCT TAT CAG ATC CTT GAT GGA GGA AAC TGC ACA CTA ATA GAT GCT CTA TTG GGA GAC CCT CAG TGT GAT GGC TTC CAG AAT AAG AAA TGG GAC CTT TTT GTT GAA CGC AGC AAA GCC TAC AGC AAC TGT TAC CCT TAT GAT GTG CCG GAT TAT GCC TCC CTT AGG TCA ATA GTT GCC TCA TCC GGC ACG CTG GAA TTT AAC AAT GAA AGC TTC AAT TGG ACT GGA GTC ACT CAA AAT GGA AAA AGC GCT TCT TGC AAA AGG GGA TCT GAT AAC AGT TTC TTT AGT AGA TTG AAT TGG TTG ACC CAC TTA AAT TAC AAA TAT CCA GCA TTG AAA GTT ACT ATG CCA AAC AAT GAA AAA TTT GAC AAA TTG TAC ATT TGG GGG GCT CAC CAC CCG GGT ACG TAC AAT GAC CAA ATC AGC CTA TAT GCT CAA GCA TCA GGA ATA ATC ACA GTC TCT ACC AAA AGA ACC CAA CAA ACT GTG ATC CCG AAT ATC GGA TCT AGA CCC AGA GTA AGG GAT ATC CCC AGC AGA ATA AGC ATC TAT TGG ACA ATA GTA AAA CCG GGA GAC ATA CTT TTG ATA AAC AGC ACA GGG AAT CTA ATT GCT CCT CGG GGT TAT TTC AAA ATA CAA AGT GGG AAA AGC TCA ATA ATG AGA TCA GAT GCA CCC ATT GGC AAA TGC AAT TCT GAA TGT ATC ACT CCA AAT GGA AGC ATT CCC AAT GAC AAA CCA TTT CAA AAT GTA AAT AGG ATC ACA TAT GGG GCC TGT CCC AGA TAT GTT AAG CAA AAC ACC CTG AAA TTG GCA ACA GGA ATG AGA AAT GTA CCA GAG AAA CAA ACT AGA GGC ATA TTT GGC GCA ATC GCG GGT TTC ATA GAA AAT GGT TGG GAG GGA ATG GTT GAT GGT TGG TAC GGT TTC AGG CAT CAA AAT TCT GAG GGA ATG GGA CAA GCA GCA GAT CTC AAA AGC ACT CAA GCA GCA ATC AAT CAA ATC AAT GGA AAG CTG AAT AGG TTG ATC GGG AAA ACC AAT GAG AAA TTC CAT CAG ATT GAA AAA GAA TTC TCA GAG GTA GAA GGG AGA ATT CAG GAC CTC GAG AAA TAT GTT GAG GAC ACC AAA ATA GAT CTC TGG TCA TAC AAC GCG GAG CTT CTT GTT GCC CTG GAG AAC CAA CAT ACA ATT GAT CTA ACT GAC TCA GAA ATG AAC AAA CTG TTT GAA AGA ACA AAG AAG CAA CTG AGG GAA AAT GCT GAG GAT ATG GGC AAT GGT TGT TTC AAA ATA TAC CAC AAA TGT GAC AAT GCC TGC ATA GGA TCA ATC AGA AAT GGA ACT TAT GAC CAT GAT GTA TAC AGA GAT GAA GCA TTT AGC AAC CGG TTC CAG ATC AAA GGT GTT GAG CTG AAG GCA GGA TAC AAA GAT TGG ATC CTA TGG ATT TCC TTT GCC ATA TCA TGT TTT TTG CTT TGT GTT GTT TTG TTG GGG TTC ATC ATG TGG GCC TGC CAA AAG GGC AAC ATT AGG TGC AAC ATT TGC ATT 
13
+A/Swine/GX_NS3106/2011     ATG AAG ACT ATC ATT GCT TTG AGC TAC ATT CTA TGT CTG GTT TTC GCT CAA AAA TTT CCT GGA AAT GAC AAC AGC ATG GCA ACG CTG TGC CTT GGG CAC CAT GCA GTA CCA AAC GGA ACG ATG GTG AAA ACA ATC ACG AAT GAC CAA ATT GAA GTT ACT AAT GCT ACT GAG CTG GTT CAG AGT TCC TCA ACA GGT GGA CTA TGC AAC AGC CCT TAT CAG ATC CTT GAT GGA GGA AAC TGC ACA CTA ATA GAT GCT CTA TTG GGA GAC CCT CAG TGT GAT GGA TTC CAG AAT AAG AAA TGG GAC CTT TTT GTT GAA CGC AGC AAA GCC TAC AGC AAC TGT TAC CCT TAT GAT GTG CCT GAT TAT GCC TCC CTT AGG TCA ATA GTT GCC TCA TCC GGC ACG CTG GAA TTT AAC AAT GAA AGC TTC AAT TGG ACT GGA GTC ACT CAA AAT GGA AAA AGC GCT TCT TGC AAA AGG GGA TCT GAT AAC AGT TTC TTT AGT AGA TTG AAT TGG TTG ACC CAC TTA AAT TAC AAA TAT CCA GCA TTG AAA GTT ACT ATG CCA AAC AAT GAA AAA TTT GAC AAA TTG TAC ATT TGG GGG GCT CAC CAC CCG GGT ACG TAC AAT GAC CAA ATC AGC CTA TAT GCT CAG GCA TCA GGA ATA ATC ACA GTC TCT ACC AAA AGA ACC CAA CAA ACT GTG ATC CCG AAT ATC GGA CCT AGA CCC AGA GTA AGG GAT ATC CCC AGC AGA ATA AGC ATC TAT TGG ACA ATA GTA AAA CCG GGA GAC ATA CTT TTG ATA AAC AGC ACA GGG AAT CTA ATT GCT CCT CGG GGT TAT TTC AAA ATA CAA AGT GGG AAA AGC TCA ATA ATG AGA TCA GAT GCA CCC ATT GGC AAA TGC AAT TCT GAA TGT ATC ACT CCA AAT GGA AGC ATT CCC AAT GAC AAA CCA TTT CAA AAT GTA AAT AGG ATC ACA TAT GGG GCC TGT CCC AGA TAT GTT AAG CAA AAC ACC CTG AAA TTG GCA ACA GGA ATG AGA AAT GTA CCA GAG AAA CAA ACT AGA GGC ATA TTT GGC GCA ATC GCG GGT TTC ATA GAA AAT GGT TGG GAG GGA ATG GTT GAT GGT TGG TAC GGT TTC AGG CAT CAA AAT TCT GAG GGA ATG GGA CAA GCA GCA GAT CTC AAA AGC ACT CAA GCA GCA ATC AAT CAA ATC AAT GGA AAG CTG AAT AGG TTG ATC GGG AAA ACC AAT GAG AAA TTC CAT CAG ATT GAA AAA GAA TTC TCA GAG GTA GAA GGG AGA ATT CAG GAC CTC GAG AAA TAT GTT GAG GAT ACC AAA ATA GAT CTC TGG TCA TAC AAC GCG GAG CTT CTT GTT GCC CTG GAG AAC CAA CAT ACA ATT GAT CTA ACT GAC TCA GAA ATG AAC AAA CTG TTT GAA AGA ACA AAG AAG CAA CTG AGG GAA AAT GCT GAG GAT ATG GGC AAT GGT TGT TTC AAA ATA TAC CAC AAA TGT GAC AAT GCC TGC ATA GGA TCA ATC AGA AAT GGA ACT TAT GAC CAT GAT GTA TAC AGA GAT GAA GCA TTT AGC AAC CGG TTC CAG ATC AAA GGT GTT GAG CTG GAG GCA GGA TAC AAA GAT TGG ATC CTA TGG ATT TCC TTT GCC ATA TCA TGT TTT TTG CTT TGT GTT GTT TTG TTG GGG TTC ATC ATG TGG GCC TGC CAA AAG GGC AAC ATT AGG TGC AAC ATT TGC ATT 
14
+A/Swine/GX_NS3108/2011     ATG AAG ACT ATC ATT GCT TTG AGC TAC ATT CTA TGT CTG GTT TTC GCT CAA AAA TTT CCT GGA AAT GAC AAC AGC ATG GCA ACG CTG TGC CTT GGG CAC CAT GCA GTA CCA AAC GGA ACG ATG GTG AAA ACA ATC ACG AAT GAC CAA ATT GAA GTT ACT AAT GCT ACT GAG CTG GTT CAG AGT TCC TCA ACA GGT GGA CTA TGC AAC AGC CCT TAT CAG ATC CTT GAT GGA GGA AAC TGC ACA CTA ATA GAT GCT CTA TTG GGA GAC CCT CAG TGT GAT GGC TTC CAG AAT AAG AAA TGG GAC CTT TTT GTT GAA CGC AGC AAA GCC TAC AGC AAC TGT TAC CCT TAT GAT GTG CCT GAT TAT GCC TCC CTT AGG TCA ATA GTT GCC TCA TCC GGC ACG CTG GAA TTT AAC AAT GAA AGC TTC AAT TGG ACT GGA GTC ACT CAA AAT GGA AAA AGC GCT TCT TGC AAA AGG GGA TCT GAT AAC AGT TTC TTT AGT AGA TTG AAT TGG TTG ACC CAC TTA AAT TAC AAA TAT CCA GCA TTG AAA GTT ACT ATG CCA AAC AAT GAA AAA TTT GAC AAA TTG TAC ATT TGG GGG GCT CAC CAC CCG GGT ACG TAC AAT GAC CAA ATC AGC CTA TAT GCT CAG GCA TCA GGA ATA ATC ACA GTC TCT ACC AAA AGA ACC CAA CAA ACT GTG ATC CCG AAT ATC GGA TCT AGA CCC AGA GTA AGG GAT ATC CCC AGC AGA ATA AGC ATC TAT TGG ACA ATA GTA AAA CCG GGA GAC ATA CTT TTG ATA AAC AGC ACA GGG AAT CTA ATT GCT CCT CGG GGT TAT TTC AAA ATA CAA AGT GGG AAA AGC TCA ATA ATG AGA TCA GAT GCA CCC ATT GGC AAA TGC AAT TCT GAA TGT ATC ACT CCA AAT GGA AGC ATT CCC AAT GAC AAA CCA TTT CAA AAT GTA AAT AGG ATC ACA TAT GGG GCC TGT CCC AGA TAT GTT AAG CAA AAC ACC CTG AAA TTG GCA ACA GGA ATG AGA AAT GTA CCA GAG AAA CAA ACT AGA GGC ATA TTT GGC GCA ATC GCG GGT TTC ATA GAA AAT GGT TGG GAG GGA ATG GTT GAT GGT TGG TAC GGT TTC AGG CAT CAA AAT TCT GAG GGA ATG GGA CAA GCA GCA GAT CTC AAA AGC ACT CAA GCA GCA ATC AAT CAA ATC AAT GGA AAG CTG AAT AGG TTG ATC GGG AAA ACC AAT GAG AAA TTC CAT CAG ATT GAA AAA GAA TTC TCA GAG GTA GAA GGG AGA ATC CAG GAC CTC GAG AAA TAT GTT GAG GAT ACC AAA ATA GAT CTC TGG TCA TAC AAC GCG GAG CTT CTT GTT GCC CTG GAG AAC CAA CAT ACA ATT GAT CTA ACT GAC TCA GAA ATG AAC AAA CTG TTT GAA AGA ACA AAG AAG CAA CTG AGG GAA AAT GCT GAG GAT ATG GGC AAT GGT TGT TTC AAA ATA TAC CAC AAA TGT GAC AAT GCC TGC ATA GGA TCA ATC AGA AAT GGA ACT TAT GAC CAT GAT GTA TAC AGA GAT GAA GCA TTT AGC AAC CGG TTC CAG ATC AAA GGT GTT GAG CTG AAG GCA GGA TAC AAA GAT TGG ATC CTA TGG ATT TCC TTT GCC ATA TCA TGT TTT TTG CTT TGT GTT GTT TTG TTG GGG TTC ATC ATG TGG GCC TGC CAA AAG GGC AAC ATT AGG TGC AAC ATT TGC ATT 
15
+A/Swine/HK_NS2810/2011     ATG AAG ACT ATC ATT GCT TTG AGC TAC ATT CTA TGT CTG GTT TTC GCT CAA AAA TTT CCT GGA AAT GAC AAC AAC ATG GCA ATG CTG TGC CTT GGG CAC CAT GCA GTA CCA AAC GGA ACG ATG GTG AAA ACA ATC ACG AAT GAC CAA ATT GAA GTT ACT AAT GCT ACT GAG CTG GTT CAG AGT TCC TCA ACA GGT GGA ATA TGC AAC AGC CCT TAT CAG ATC CTT GAT GGA GGA AAC TGC ACA CTA ATA GAT GCT CTA TTG GGA GAC CCT CAG TGT GAT GGC TTC CAG AAT AAG AAA TGG GAC CTT TTT GTT GAA CGC AGC AAA GCC TAC AGC AAC TGT TAC CCT TAT GAT GTG CCG GAT TAT GCC TCC CTT AGG TCA ATA GTT GCC TCA TCC GGC ACG CTG GAA TTT AAC AAT GAA AGC TTC AAT TGG ACT GGA GTC ACT CAA AAT GGA AAA AGC GCT TCT TGC AAA AGG GGA TCT GAT AAC AGT TTC TTT AGT AGA TTG AAT TGG TTG ACC CAC TTA AAT TAC AAA TAT CCA GCA TTG AAA GTT ACT ATG CCA AAC AAT GAA AAA TTT GAC AAA TTG TAC ATT TGG GGG GCT CAC CAC CCG GGT ACG TAC AAT GAC CAA ATC AGC CTA TAT GCT CAA GCA TCA GGA ATG ATC ACA GTC TCT ACC AAA AGA ACC CAA CAA ACT GTG ATC CCG AAT ATC GGA TCT AGA CCC AGA GTA AGG GAT ATC CCC AGC AGA ATA AGC ATC TAT TGG ACA ATA GTA AAA CCG GGA GAC ATA CTT TTG ATT AAC AGC ACA GGG AAT CTA ATT GCT CCT CGG GGT TAT TTC AAA TTA CAA AAT GGG AAA AGC TCA ATA ATG AGA TCA GAT GCA CCC ATT GGC AAA TGC AGT TCT GAA TGT ATC ACC CCA AAT GGA AGC ATT CCC AAT GAC AGA CCA TTT CAA AAT GTA AAT AGG ATC ACA TAT GGG GCC TGT CCC AGA TAT GTT AAG CAA AAC ACC CTG AAA TTG GCA ACA GGA ATG AGA AAT GTA CCA GAT AAA CAA ACT AGA GGC ATA TTT GGC GCA ATC GCG GGT TTC ATA GAA AAT GGT TGG GAG GGA ATG ATT GAT GGT TGG TAC GGT TTC AGG CAC CAA AAT TCT GAG GGA ATG GGA CAA GCA GCA GAT CTC AAA AGC ACT CAA GCA GCA ATC AAT CAA ATC AAT GGA AAG CTG AAT AGG TTG ATC GGG AAA ACC AAT GAG AAA TTC CAT CAG ATT GAA AAA GAA TTC TCA GAG GTA GAA GGA AGA ATT CAG GAC CTC GAG AAA TAT GTT GAG GAC ACC AAA ATA GAT CTC TGG TCA TAC AAC GCG GAG CTT CTT GTT GCC CTG GAG AAC CAA CAT ACA ATT GAT CTA ACT GAC TCA GAA ATG AAC AAA CTG TTT GAA AGA ACA AAG AAG CAA CTG AGG GAA AAT GCT GAG GAT ATG GGC AAT GGT TGT TTC AAA ATA TAC CAC AAA TGT GAC AAT GCC TGC ATA GGA TCA ATC AGA AAT GGA ACT TAT GAC CAT GAT GTA TAC AGA GAT GAA GCA TTG AGC AAC CGG TTC CAG ATC AAA GGT GTT GAG CTG AAG GCA GGA TAC AAA GAT TGG ATC CTA TGG ATT TCC TTT GCC ATA TCA TGT TTT TTG CTT TGT GTT GTT TTG TTG GGG TTC ATC ATG TGG GCC TGC CAA AAA GGC AAC ATT AGG TGC AAC ATT TGC ATT 
16
+A/Swine/HK/2857/2011       ATG AAG ACT ATC ATT GCT TTG AGC TAC ATT CTA TGT CTG GTT TTC GCT CAA AAA TTT CCT GGA AAT GAC AAC AGC ATG GCA ACG CTG TGC CTT GGG CAC CAT GCA GTA CCA AAC GGA ACG ATG GTG AAA ACA ATA GCG AAT GAC CAA ATT GAA GTC ACT AAT GCT ACT GAG CTG GTT CAG AGT TCC TCA ACA GGT GGA ATA TGC AAC AGC CCT CAT CAG ATC CTT GAT GGA GGA AAC TGC ACA CTA ATA GAT GCT CTA TTG GGA GAC CCT CAG TGT GAT GGC TTC CAG AAT AAG AAA TGG GAC CTT TTT GTT GAA CGC AGC AAA GCC TAC AGC AAC TGT TAC CCT TAT GAT GTG CCG GAT TAT ACA TCC CTT AGG TCA ATA GTT GCC TCA TCC GGC ACA CTG GAA TTT AAC AAT GAA AGC TTC AAT TGG ACT GGA GTC ACT CAA AAT GGA AAA AGC GCT TCT TGC AAA AGG GGA TCT GAC AAC AGT TTC TTT AGT AGA TTG AAT TGG TTG ACC CAC TTA AAT TAC AAA TAT CCA GCA TTG AAA GTT GCT ATG CCA AAC AAT GAA AAA TTT GAC AAA TTG TAC ATT TGG GGG GTT CAC CAC CCG GGT ACG TAC AAT GAC CAA ATC AGC CTA TAT GCT CAA GCA TCA GGA ATA ATC ACA GTC TCT ACC AAA AGA AAC CAA CAA ACT GTG ATC CCA AAT ATC GGA TCT AGA CCC AGA GTA AGG GAT ATC CCC AGC AGA ATA AGC ATC TAT TGG ACA ATA GTA AAA CCA GGA GAC ATA CTT TTG ATT AAC AGC ACA GGG AAT CTA ATT GCT CCT CGG GGT TAC TTC AAA ATA CAA AGT GGG AAA AGC TCA ATA ATG AGA TCA GAT GCA CCC ATT GGC AAA TGC AAT TCT GAA TGT ATC ACT CCA AAT GGA AGC ATT CCC AAT GAC AAA CCA TTT CAA AAT GTA AAT AGG ATC ACA TAT GGG GCC TGT CCC AGG TAT GTT AAG CAA AAC ACC CTA AAA TTG GCA ACA GGA ATG AGA AAT GTT CCA GAG AAA CAA ACT AGA GGC ATA TTT GGC GCA ATC GCG GGT TTC ATA GAA AAT GGT TGG GAG GGA ATG GTT GAT GGT TGG TAC GGT TTC AGG CAT CAA AAT TCT GAG GGA ATG GGA CAA GCA GCA GAT CTC AAA AGC ACT CAA GCA GCG GTC AAT CAA ATC AAT GGA AAG CTG AAT AGG TTG ATC GGG AAA ACC AAT GAG AAA TTC CAT CAG ATT GAA AAA GAA TTC TCA GAG GTA GAA GGG AGA ATT CAG GAC CTC GAG AAA TAT GTT GAG GAC ACC AAA ATA GAT CTC TGG TCA TAC AAC GCG GAG CTT CTT GTT GCC CTG GAG AAC CAA CAT ACA ATT GAT CTA ACT GAC TCA GAA ATG GAC AAA CTG TTT GAA AGA ACA AAG AAG CAA CTG AGG GAA AAT GCT GAG GAT ATG GGC AAT GGT TGT TTC AAA ATA TAC CAC AAA TGT GAC AAT GCC TGC ATA GGA TCA ATC AGA AAT GGA ACT TAT GAC CAT GAT ATA TAC AGA GAT GAA GCA TTG AGC AAC CGG TTC CAG ATC AAA GGT GTT GAG CTG AAG GCA GGA TAC AAA GAT TGG ATC CTA TGG ATT TCC TTT GCC ATA TCA TGT TTT TTG CTT TGT GTT GTT TTG TTG GGG TTC ATC ATG TGG GCC TGC CAA AAG GGC AAC ATT AGG TGC AAC ATT TGC ATT 
17
+A/Swine/HK/3238/2011       ATG AAG ACT ATC ATT GCT TTG AGC TAC ATT CTA TGT CTG GTT TTC GCT CAA AAA TTT CCT GGA AAT GAC AAC AAC ATG GCA ATG CTG TGC CTT GGG CAC CAT GCA GTA CCA AAC GGA ACG ATG GTG AAA ACA ATC ACG AAT GAC CAA ATT GAA GTT ACT AAT GCT ACT GAG CTA GTT CAG AGT TCC TCA ACA GGT GGA ATA TGC AAC AGC CCT TAT CAG ATC CTT GAT GGA GGA AAC TGC ACA CTA ATA GAT GCT CTA TTG GGA GAC CCT CAG TGT GAT GGC TTC CAG AAT AAG AAA TGG GAC CTT TTT GTT GAA CGC AGC AAA GCC TAC AGC AAC TGT TAC CCT TAT GAT GTG CCG GAT TAT GCC TCC CTT AGG TCA ATA GTT GCC TCA TCC GGC ACG CTG GAA TTT AAC AAT GAA AGC TTC AAT TGG ACT GGA GTC ACT CAA AAT GGA AAA AGC GCT TCT TGC AAA AGG GGA TCT GAT AAC AGT TTC TTT AGT AGA TTG AAT TGG TTG ACC CAC TTA AAT TAC AAA TAT CCA GCA TTG AAA GTT ACT ATG CCA AAC AAT GAA AAA TTT GAC AAA TTG TAC ATT TGG GGG GCT CAC CAC CCG GGT ACG TAC AAT GAC CAA ATC AGC CTA TAT GCT CAA GCA TCA GGA ATA ATC ACA GTC TCT ACC AAA AGA ACC CAA CAA ACT GTG ATC CCG AAT ATC GGA TCT AGA CCC AGA GTA AGG GAT ATC CCC AGC AGA ATA AGC ATC TAT TGG ACA ATA GTA AAA CCG GGA GAC ATA CTT TTG ATT AAC AGC ACA GGG AAT CTA ATT GCT CCT CGG GGT TAT TTC AAA TTA CAA AAT GGG AAA AGC TCA ATA ATG AGA TCA GAT GCA CCC ATT GGC AAA TGC AAT TCT GAA TGT ATC ACC CCA AAC GGA AGC ATT CCC AAT GAC AGA CCA TTT CAA AAT GTA AAT AGG ATC ACA TAT GGG GCC TGT CCC AGA TAT GTT AAG CAA AAC ACC CTG AAA TTG GCA ACA GGA ATG AGA AAT GTA CCA GAG AAA CAA ACT AGA GGC ATA TTT GGC GCA ATC GCG GGT TTC ATA GAA AAT GGT TGG GAG GGA ATG GTT GAT GGT TGG TAC GGT TTC AGG CAC CAA AAT TCT GAG GGA ATG GGA CAA GCA GCA GAT CTC AAA AGC ACT CAA GCA GCA ATC AAT CAA ATC AAT GGA AAG CTG AAT AGG TTG ATC GGG AAA ACC AAT GAG AAA TTC CAT CAG ATT GAA AAA GAA TTC TCA GAG GTA GAA GGA AGA ATT CAG GAC CTC GAG AAA TAT GTT GAG GAC ACC AAA ATA GAT CTC TGG TCA TAC AAC GCG GAG CTT CTT GTT GCC CTG GAG AAC CAA CAT ACA ATT GAT CTA ACT GAC TCA GAA ATG AAC AAA CTG TTT GAA AGA ACA AAG AAG CAA CTG AGG GAA AAT GCT GAG GAT ATG GGC AAT GGT TGT TTA AAA ATA TAC CAC AAA TGT GAC AAT GCC TGC ATA GGA TCA ATC AGA AAT GGA ACT TAT GAC CAT GAC GTA TAC AGA GAT GAA GCA TTG AGC AAC CGG TTC CAG ATC AAA GGT GTT GAG CTG AAG GCA GGA TAC AAA GAT TGG ATC CTA TGG ATT TCC TTT GCC ATA TCA TGT TTT TTG CTT TGT GTT GTT TTG TTG GGG TTC ATC ATG TGG GCC TGC CAA AAG GGC AAC ATT AGG TGC AAC ATT TGC ATT 
18
+A/Swine/HK/3700/2011       ATG AAG ACT ATT ATT GCT TTG AGC TAC ATT CTA TGT CTG GTT TTC GCT CAA AAA TTT CCT GGA AAT GAC AAC AAC ATG GCA ATG CTG TGC CTT GGG CAC CAT GCA GTA CCA AAC GGA ACG ATG GTG AAA ACA ATC ACG AAT GAC CAA ATT GAA GTT ACT AAT GCT ACT GAG CTG GTT CAG AGT TCC TCA ACA GGT GGA ATA TGC AAC AGC CCT TAT CAG ATC CTT GAT GGA GGA AAC TGC ACA CTA ATA GAT GCT ATA TTG GGA GAC CCT CAG TGT GAT GGC TTC CAG AAT AAG AAA TGG GAC CTT TTT GTT GAA CGC AGC AAA GCC TAC AGC AAC TGT TAC CCT TAT GAT GTG CCG GAT TAT GCC TCC CTT AGG TCA ATA GTT GCC TCA TCC GGC ACG CTG GAA TTT AAC AAT GAA AGC TTC AAT TGG ACT GGA GTC ACT CAA AAT GGA AAA AGC GCT TCT TGC AAA AGG GGA TCT GAT AAC AGT TTC TTT AGT AGA TTG AAT TGG TTG ACC CAC TTA AAT TAC AAA TAT CCA GCA TTG AAA GTT ACT ATG CCA AAC AAT GAA AAA TTT GAC AAA TTG TAC ATT TGG GGG GCT CAC CAC CCG GGT ACG TAC AAT GAC CAA ATC AGC CTA TAT GCT CAA GCA TCA GGA ATA ATC ACA GTC TCT ACC AAA AGA ACC CAA CAA ACT GTG ATC CCG AAT ATC GGA TCT AGA CCC AGA GTA AGG GAT ATC CCC AGC AGA ATA AGC ATC TAT TGG ACA ATA GTA AAA CCG GGG GAC ATA CTT TTG ATT AAC AGC ACA GGG AAT CTA ATT GCT CCT CGG GGT TAT TTC AAA TTA CAA AAT GGG AAA AGC TCA ATA ATG AGA TCA GAT GCA CCC ATT GAC AAA TGC AAT TCT GAA TGT ATC ACC CCA AAT GGA AGC ATT CCC AAT GAC AGA CCA TTT CAA AAT GTA AAT AGG ATC ACA TAT GGG GCC TGT CCC AGA TAT GTT AAG CAA AAC ACC CTG AAA TTG GCA ACA GGA ATG AGA AAT GTA CCA GAG AAA CAA ACT AGA GGC ATA TTT GGC GCA ATC GCG GGT TTC ATA GAA AAT GGT TGG GAG GGA ATG GTT GAT GGT TGG TAC GGT TTC AGG CAC CAA AAT TCT GAG GGA ATG GGA CAA GCA GCA GAT CTC AAA AGC ACT CAA GCA GCA ATC AAT CAA ATC AAT GGA AAG CTG AAT AGG TTG ATC GGG AAA ACC AAT GAG AAA TTC CAT CAG ATT GAA AAA GAA TTC TCA GAG GTA GAA GGA AGA ATT CAG GAC CTC GAG AAA TAT GTT GAG GAC ACC AAA ATA GAT CTC TGG TCA TAC AAC GCG GAG CTT CTT GTT GCC CTG GAG AAC CAA CAT ACA ATT GAT CTA ACT GAC TCA GAA ATG AAC AAA CTG TTT GAA AGA ACA AAG AAG CAA CTG AGG GAA AAT GCT GAG GAT ATG GGC AAT GGT TGT TTC AAA ATA TAC CAC AAA TGT GAC AAT GCC TGC ATA GGA TCA ATC AGA AAT GGA ACT TAT GAC CAT GAT GTA TAC AGA GAT GAA GCA TTG AGC AAC CGG TTC CAG ATC AAA GGT GTT GAG CTG AAG GCA GGA TAC AAA GAT TGG ATC CTA TGG ATT TCC TTT GCC ATA TCA TGT TTT TTG CTT TGT GTT GTT TTG TTG GGG TTC ATC ATG TGG GCC TGC CAA AAG GGC AAC ATT AGG TGC AAC ATT TGC ATT 
19
+A/Swine/HK/168/2012        ATG AAG ACT ATT ATT GCT TTG AGC TAC ATT CTA TGT CTG GTT TTC GCT CAA AAA TTT CCT GGA AAT GAC AAC AAC ATG GCA ATG CTG TGC CTT GGG CAC CAT GCA GTA CCA AAC GGA ACG ATG GTG AAA ACA ATC ACG AAT GAC CAA ATT GAA GTT ACT AAT GCT ACT GAG CTG GTT CAG AGT TCC TCA ACA GGT GGA ATA TGC AAC AGC CCT TAT CAG ATC CTT GAT GGA GGA AAC TGC ACA CTA ATA GAT GCT ATA TTG GGA GAC CCT CAG TGT GAT GGC TTC CAG AAT AAG AAA TGG GAC CTT TTT GTT GAA CGC AGC AAA GCC TAC AGC AAC TGT TAC CCT TAT GAT GTG CCG GAT TAT GCC TCC CTT AGG TCA ATA GTT GCC TCA TCC GGC ACG CTG GAA TTT AAC AAT GAA AGC TTC AAT TGG ACT GGA GTC ACT CAA AAT GGA AAA AGC GCT TCT TGC AAA AGG GGA TCT GAT AAC AGT TTC TTT AGT AGA TTG AAT TGG TTG ACC CAC TTA AAT TAC AAA TAT CCA GCA TTG AAA GTT ACT ATG CCA AAC AAT GAA AAA TTT GAC AAA TTG TAC ATT TGG GGG GCT CAC CAC CCG GGT ACG TAC AAT GAC CAA ATC AGC CTA TAT GCT CAA GCA TCA GGA ATA ATC ACA GTC TCT ACC AAA AGA ACC CAA CAA ACT GTG ATC CCG AAT ATC GGA TCT AGA CCC AAA GTA AGG GAT ATC CCC AGC AGA ATA AGC ATC TAT TGG ACA ATA GTA AAA CCG GGA GAC ATA CTT TTG ATT AAC AGC ACA GGG AAT CTA ATT GCT CCT CGG GGT TAT TTC AAA TTA CAA AAT GGG AAA AGC TCA ATA ATG AGA TCA GAT GCA CCC ATT GGC AAA TGC AAT TCT GAA TGT ATC ACC CCA AAT GGA AGC ATT CCC AAT GAC AGA CCA TTT CAA AAT GTA AAT AGG ATC ACA TAT GGG GCC TGT CCC AGA TAT GTT AAG CAA AAC ACC CTG AAA TTG GCA ACA GGA ATG AGA AAT GTA CCA GAG AAA CAA ACT AGA GGC ATA TTT GGC GCA ATC GCG GGT TTC ATA GAA AAT GGT TGG GAG GGA ATG GTT GAT GGT TGG TAC GGT TTC AGG CAC CAA AAT TCT GAG GGA GTG GGA CAA GCA GCA GAT CTC AAA AGC ACT CAA GCA GCA ATC AAT CAA ATC AAT GGA AAG CTG AAT AGG TTG ATC GGG AAA ACC AAT GAG AAA TTC CAT CAG ATT GAA AAA GAA TTC TCA GAG GTA GAA GGA AGA ATT CAG GAC CTC GAG AAA TAT GTT GAG GAC ACC AAA ATA GAT CTC TGG TCA TAC AAC GCG GAG CTT CTT GTT GCC CTG GAG AAC CAA CAT ACA ATT GAT CTA ACT GAC TCA GAA ATG AAC AAA CTG TTT GAA AGA ACA AAG AAG CAA CTG AGG GAA AAT GCT GAG GAT ATG GGC AAT GGT TGT TTC AAA ATA TAC CAC AAA TGT GAC AAT GCC TGC ATA GGA TCA ATC AGA AAT GGA ACT TAT GAC CAT GAT GTA TAC AGA GAT GAA GCA TTG AGC AAC CGG TTC CAG ATC AAA GGT GTT GAG CTG AAG GCA GGA TAC AAA GAT TGG ATC CTA TGG ATT TCC TTT GCC ATA TCA TGT TTT TTG CTT TGT GTT GTT TTG TTG GGG TTC ATC ATG TGG GCC TGC CAA AAG GGC AAC ATT AGG TGC AAC ATT TGC ATT 
20
+A/Swine/HK/459/2012        ATG AAG ACT ATC ATT GCT TTG AGC TAC ATT CCA TGT CTG GTT TTC GCT CAA AAA TTT CCT GGA AAT GAC AAC AAC ATG GCA ATG CTG TGC CTT GGG CAC CAT GCA GTA CCA AAC GGG ACG ATG GTG AAA ACA ATC ACG AAT GAC CAA ATT GAA GTT ACT AAT GCT ACT GAG CTG GTT CAG AGT TCC TCA ACA GGT GGA ATA TGC AAC AGC CCT TAT CAG GTC CTT GAT GGA GGA AAC TGC ACA CTA ATA GAT GCT CTA TTG GGA GAC CCT CAG TGT GAT GGC TTC CAG AAT AAG AAA TGG GAC CTT TTT GTT GAA CGC AGC AAA GCC TAC AGC AAC TGT TAC CCT TAT GAT GTG CCG GAT TAT GCC TCC CTT AGG TCA ATA GTT GCC TCA TCC GGC ACG CTG GAA TTT AAC AAT GAA AGC TTC AAT TGG ACT GGA GTC ACT CAA AAT GGA AAA AGC GCT TCT TGC AAA AGG GGA TCT GAT AAC AGT TTC TTT AGT AGA TTG AAT TGG TTG ACC CAC TTA AAT TAC AAA TAT CCA GCA TTG AAA GTT ACT ATG CCA AAC AAT GAA AAA TTT GAC AAA TTG TAC ATT TGG GGG GCT CAC CAC CCG GGT ACG TAC AAT GAC CAA ATC AGC CTA TAT GCT CAA GCA TCA GGA ATA ATC ACA GTC TCT ACC AAA AGA ACC CAA CAA ACT GTG ATC CCG AAC ATC GGA TCT AGA CCC AGA GTA AGG GAT ATC CCC AGC AGA ATA AGC ATA TAT TGG ACA ATA GTA AAA CCG GGA GAC ATA CTA TTG ATT AAC AGC ACA GGG AAT CTA ATT GCT CCT CGG GGT TAT TTC AAA TTA CAA AAT GGG AAA AGC TCA ATA ATG AGA TCA GAT GCA CCC ATT GGC AAA TGC GAT TCT GAA TGT ATC ACC CCA AAT GGA AGC ATT CCC AAT GAC AGA CCA TTT CAA AAT GTA AAT AGG ATC ACA TAT GGG GCC TGT CCC AGA TAT GTT AAG CAA AAC ACC CTG AAA TTG GCA ACA GGA ATG AGA AAT GTA CCA GAG AAA CAA ACT AGA GGC ATA TTT GGC GCA ATC GCG GGT TTC ATA GAA AAT GGT TGG GAG GGA ATG GTT GAT GGT TGG TAC GGT TTC AGG CAC CAA AAT TCT GAG GGA ATG GGA CAA GCA GCA GAT CTC AAA AGC ACT CAA GCA GCA ATC AAT CAA ATC AAT GGA AAG CTG AAT AGG TTG ATC GGG AAA ACC AAT GAG AAA TTC CAT CAG ATT GAA AAA GAA TTC TCA GAG GTA GAA GGA AGA ATT CAG GAC CTC GAG AAA TAT GTT GAG GAC ACC AAA ATA GAT CTC TGG TCA TAC AAC GCG GAG CTT CTT GTT GCC CTG GAG AAC CAA CAT ACA ATT GAT CTA ACT GAC TCA GAA ATG AAC AAA CTG TTT GAA AGA ACA AAG AAG CAA CTG AGG GAA AAT GCT GAG GAT ATG GGC AAT GGT TGT TTC AAA ATA TAC CAC AAA TGT GAC AAT GCC TGC ATA GGA TCA ATC AGA AAT GGA ACT TAT GAC CAT GAT GTA TAC AGA GAT GAA GCA TTG AGC AAC CGG TTC CAG ATT AAA GGT GTT GAG CTG AAG GCA GGA TAC AAA GAT TGG ATC CTA TGG ATT TCC TTT GCC ATA TCA TGT TTT TTG CTT TGT GTT GTT TTG TTG GGG TTC ATC ATG TGG GCC TGC CAA AAG GGC AAC ATT AGG TGC AAC ATT TGC ATT 
21
+A/Swine/HK/1071/2012       ATG AAG ACT ATC ATT GCT TTG AGC TAC ATT CTA TGT CTG GTT TTC GCT CAA AAA TTT CCT GGA AAT GAC AAC AGC ATG GCA ACG CTG TGC CTT GGG CAC CAT GCA GTA CCA AAC GGA ACG ATG GTG AAA ACA ATA ACG AAT GAC CAA ATT GAA GTC ACT AAT GCT ACT GAG CTG GTT CAG AGT TCC TCA ACA GGT GGA ATA TGC AAC AGC CCT CAT CAG ATC CTT GAT GGA GGA AAC TGC ACG TTA ATA GAT GCT CTA TTG GGA GAC CCT CAG TGT GAT GGC TTC CAG AAT AAG AAA TGG GAC CTT TTT GTT GAA CGC AGC AAA GCC TAC AGC AAC TGT TAC CCT TAT GAT GTG CCG GAT TAT ACA TCC CTT AGG TCA ATA GTT GCC TCA TCC GGC ACA CTG GAA TTT AAC AAT GAA AGC TTC AAT TGG ACT GGA GTC ACT CAA AAT GGG AAA AGC GCT TCT TGC AAA AGA GGA TCT GAC AAC AGT TTC TTT AGT AGA TTG AAT TGG TTG ACC CAC TTA AAT TAC AAA TAT CCA GCA TTG AAA GTT ACT ATG CCA AAC AAT GAA AAA TTT GAC AAA TTG TAC ATT TGG GGG GTT CAC CAC CCG GGT ACG TAC AAT GAC CAA ATC AGC CTA TAT GCT CAA GCA TCA GGA ATA ATC ACA GTC TCT ACC AAA AGA AAC CAA AAA ACT GTG ATC CCA AAT ATC GGA TCT AGA CCC AGA GTA AGG GAT ATC CCC AGC AGA ATA AGC ATC TAT TGG ACA ATA GTA AAA CCA GGA GAC ATA CTT TTG ATT AAC AGC ACA GGG AAT CTT ATT GCT CCT CGG GGT TAC TTC AAA ATA CAA AGT GGG AAA AGC TCA ATA ATG AGA TCA GAT GCA CCC ATT GGC AAA TGC AAT TCT GAA TGT ATC ACT CCA AAT GGA AGC ATT CCC AAT GAC AAA CCA TTT CAA AAT GTA AAT AGG ATC ACA TAT GGG GCT TGT CCC AGG TAT GTT AAG CAA AAC ACC CTA AAA TTG GCA ACA GGA ATG AGA AAT GTT CCA GAG AAA CAA ACT AGA GGC ATA TTT GGC GCA ATC GCG GGT TTC ATA GAA AAT GGT TGG GAG GGA ATG GTT GAT GGT TGG TAC GGT TTC AGG CAT CAA AAT TCT GAG GGA ATG GGR CAA GCA GCA GAT CTC AAA AGC ACT CAA GCA GCG GTC GAT CAA ATC AAT GGA AAG CTG AAT AGG TTG ATC GGG AAG ACC AAT GAG AAA TTC CAT CAG ATT GAA AAA GAA TTC TCA GAG GTA GAA GGG AGA ATT CAA GAC CTC GAG AAA TAT GTT GAG GAC ACC AAA ATA GAT CTC TGG TCA TAC AAC GCG GAG CTT CTT GTT GCC CTG GAG AAC CAA CAT ACA ATT GAT CTA ACT GAC TCA GAA ATG GAC AAA CTG TTT GAA AGA ACA AAG AAG CAA CTG AGG GAA AAT GCT GAG GAT ATG GGC AAT GGT TGT TTC AAA ATA TAC CAC AAA TGT GAC AAT GCC TGC ATA GGA TCA ATC AGA AAT GGA ACT TAT GAC CAT GAT ATA TAC AGA GAT GAA GCA TTG AGC AAC CGG TTC CAG ATC AAA GGT GTT GAG CTG AAG GCA GGA TAC AAA AAT TGG ATC CTA TGG ATT TCC TTT GCC ATA TCA TGT TTT TTG CTT TGT GTT GTT TTG TTG GGG TTC ATC ATG TGG GCC TGC CAA AAG GGC AAC ATT AGG TGC AAC ATT TGC ATT 
22
+A/Swine/HK/1284/2012       ATG AAG ACT ATC ATT GCT TTG AGC TAC ATT CTA TGT CTG GTT TTC GCT CAA AAA TTT CCT GGA AAT GAC AAC AAC ATG GCA ATG CTG TGC CTT GGG CAC CAT GCA GTA CCA AAC GGA ACG ATG GTG AAA ACA ATC ACG AAT GAC CAA ATT GAA GTT ACT AAT GCT ACT GAG CTG GTT CAG AGT TCC TCA ACA GGT GGA ATA TGC AAC AAC CCT TAT CAG ATC CTT GAT GGA GGA AAC TGC ACA TTA ATA GAT GCT CTA TTG GGA GAC CCT CAG TGT GAT GGC TTC CAG AAT AAG AAA TGG GAC CTT TTT GTT GAA CGC AGC AAA GCC TAC AGC AAC TGT TAC CCT TAT GAT GTG CCG GAT TAT GCC TCC CTT AGG TCA ATA GTT GCC TCA TCC GGC ACG CTG GAA TTT AAC AAT GAA AGC TTC AAT TGG ACT GGA GTC ACT CAA AAT GGA AAA AGC GCT TCT TGC AAA AGG GGA TCT GAT AAC AGT TTC TTT AGT AGA TTG AAT TGG TTG ACC CAC TTA AAT TAC AAA TAT CCA GCA TTG AAA GTT ACT ATG CCA AAC AAT GAA AAA TTT GAC AAA TTG TAC ATT TGG GGG GCT CAC CAC CCG GGT ACG TAC AAT GAC CAA ATC AGC CTA TAT GCT CAA GCA TCA GGA ATA ATC ACA GTC TCT ACC AAA AGA ACC CAA CAA ACT GTG ATC CCG AAT ATC GGA TCT AGA CCC AGA GTA AGG GAT ATC CCC AGC AGA ATA AGC ATC TAT TGG ACA ATA GTA AAA CCG GGA GAC ATA CTT TTG ATT AAC AGC ACA GGG AAT CTA ATT GCT CCT CGG GGT TAT TTC AAA TTA CAA AAT GGG AAA AGC TCA ATA ATG AGA TCA GAT GCA CCC ATT GGC AAA TGC AAT TCT GAA TGT ATC ACC CCA AAT GGA AGC ATT CCC AAT GAC AGA CCA TTT CAA AAT GTA AAT AGG ATC ACA TAT GGG GCC TGT CCC AGA TAT GTT AAG CAA AAC ACC CTG AAA TTG GCA ACA GGA ATG AGA AAT GTA CCA GAG AAA CAA ACT AGA GGC ATA TTT GGC GCA ATC GCG GGT TTC ATA GAA AAT GGT TGG GAG GGA ATG GTT GAT GGT TGG TAC GGT TTC AGG CAC CAA AAT TCT GAG GGA ATG GGA CAA GCA GCA GAT CTT AAA AGC ACT CAA GCA GCA ATC AAT CAA ATC AAT GGA AAG CTG AAT AGG TTG ATC GGG AAA ACC AAT GAG AAA TTC CAT CAG ATT GAA AAA GAA TTC TCA GAG GTA GAA GGA AGA ATT CAG GAC CTC GAG AAA TAT GTT GAG GAC ACC AAA ATA GAT CTC TGG TCA TAC AAC GCG GAG CTT CTT GTT GCC CTG GAG AAC CAA CAT ACA ATT GAT CTA ACT GAC TCA GAA ATG AAC AAA CTG TTT GAA AGA ACA AAG AAG CAA CTG AGG GAA AAT GCT GAG GAT ATG GGC AAT GGT TGT TTC AAA ATA TAC CAC AAA TGT GAC AAT GCC TGC ATA GGA TCA ATC AGA AAT GGA ACT TAT GAC CAT GAT GTA TAC AGA GAT GAA GCA TTG AGC AAC CGG TTC CAG ATC AAA GGT GTT GAG CTG AAG GCA GGA TAC AAA GAT TGG ATC CTA TGG ATT TCC TTT GCC ATA TCA TGT TTT TTG CTT TGT GTT GTT TTG TTG GGG TTC ATC ATG TGG GCC TGC CAA AAG GGC AAC ATT AGG TGC AAC ATT TGC ATT 
23
+A/Swine/GX/650/2012        ATG AAG ACT ATC ATT GCT TTG AGC TAC ATT CTA TGT CTG GTT TTC GCT CAA AAA TTT CCT GGA AAT GAC AAC AAC ATG GCA ATG CTG TGC CTT GGG CAC CAT GCA GTA CCA AAC GGA ACG ATG GTG AAA ACA ATC ACG AAT GAC CAA ATT GAA GTT ACT AAT GCT ACT GAG CTG GTT CAG AGT TCC TCA ACA GGT GGA ATA TGC AAC AGC CCT TAT CAG ATC CTT GAT GGA GGA AAC TGC ACA CTA ATA GAT GCT CTA TTG GGA GAC CCT CAG TGT GAT AGC TTC CAG AAT AAG AAA TGG GAC CTT TTT GTT GAA CGC AGC AAA GCC TAC AGC AAC TGT TAC CCT TAT GAT GTG CCG GAT TAT GCC TCC CTT AGG TCA ATA GTT GCC TCA TCC GGC ACA CTG GAA TTT AAC AAT GAA AGC TTC AAT TGG ACT GGA GTC ACT CAA AAT GGA AAA AGC GCT TCT TGC AAA AGG GGA TCT GAT AAC AGT TTC TTT AGT AGA TTG AAT TGG TTG ACC CAC TTA AAT TAC AAA TAT CCA GCA TTG AAA GTT ACT ATG CCA AAC AAT GAA AAA TTT GAC AAA TTA TAC ATT TGG GGG GCT CAC CAC CCG GGT ACG TAC AAT GAC CAA ATC AGC CTA TAT GCT CAA GCA TCA GGA ATA ATC ACA GTC TCT ACC AAA AGA ACC CAA CAA ACT GTG ATC CCG AAT ATC GGA TCT AGA CCC AGA GTA AGG GAT ATC CCC AGC AGA ATA AGC ATC TAT TGG ACA ATA GTA AAA CCG GGA GAC ATA CTT TTG ATT AAC AGC ACA GGG AAT CTA ATT GCT CCT CGG GGT TAT TTC AAA TTA CAA AAT GGG AAA AGC TCA ATA ATG AGA TCA GAT GCA CCC ATT GGC AAA TGC AAT TCT GAA TGT ATC ACC CCA AAT GGA AGC ATT CCC AAT GAC AGA CCA TTT CAA AAT GTA AAT AGG ATC ACA TAT GGG ACC TGT CCC AGA TAT GTT AAG CAA AAC ACC CTG AAA TTG GCA ACA GGA ATG AGA AAT GTA CCA GAG AAA CAA ACT AGA GGC ATA TTT GGC GCA ATC GCG GGT TTC ATA GAA AAT GGT TGG GAG GGA ATG GTT GAT GGT TGG TAC GGT TTC AGG CAC CGA AAT TCT GAG GGA ATG GGA CAA GCA GCA GAT CTC AAA AGC ACT CAA GCA GCA ATT AAT CAA ATC AAT GGA AAG CTG AAT AGG TTG ATC GGG AAA ACC AAT GAG AAA TTC CAT CAG ATT GAA AAA GAA TTC TCA GAG GTA GAA GGA AGA ATT CAG GAC CTC GAG AAA TAT GTT GAG GAC ACC AAA ATA GAT CTC TGG TCA TAC AAC GCG GAG CTT CTT GTT GCC CTG GAG AAC CAA CAT ACA ATT GAT CTA ACT GAC TCA GAA ATG AAC AAA CTG TTT GAA AGA ACA AAG AAG CAA CTG AGG GAA AAT GCT GAA GAT ATG GGC AAT GGT TGT TTC AAA ATA TAC CAC AAA TGT GAC AAT GCC TGC ATA GGA TCA ATC AGA AAT GGA ACT TAT GAC CAT GAT GTA TAC AGA GAT GAG GCA TTG AGC AAC CGG TTC CAG ATC AAA GGT GTT GAG CTG AAG GCA GGA TAC AAA GAT TGG ATC CTA TGG ATT TCC TTT GCC ATA TCA TGT TTT TTG CTT TGT GTT GTT TTG TTG GGG TTC ATC ATG TGG GCC TGC CAA AAG GGC AAC ATT AGG TGC AAC ATT TGC ATT 
24
+A/Swine/GX_NS1409/2012     ATG AAG ACT ATC ATT GCT TTG AGC TAC ATT CTA TGT CTG GTT TTC GCT CAA AAA TTT CCT GGA AAT GAC AAC AAC ATG GCA ATG CTG TGC CTT GGG CAC CAT GCA GTG CCA AAC GGA ACG ATG GTG AAA ACA ATC ACG AAT GAC CAA ATT GAA GTT ACT AAT GCT ACC GAG CTG GTT CAG AAT TCC TCA ACA GGT GGA ATA TGC AAC AGC CCT TAT CAG ATC CTT GAT GGA GGA AAC TGC ACA CTA ATA GAT GCT CTA TTG GGA GAC CCT CAG TGT GAT GGC TTC CAG AAT AAG AAA TGG GAC CTT TTT GTT GAA CGC AGC AAA GCC TAC AGC AAC TGT TAC CCT TAT GAT GTG CCG GAT TAT GCC TCC CTT AGG TCA ATA GTT GCC TCA TCC GGC ACG CTG GAA TTT AAC AAT GAA AGC TTC AAT TGG ACT GGA GTC ACT CAA AAT GGA AAA AGC GCT TCT TGC AAA AGG GGA TCT GAT AAC AGT TTC TTT AGT AGA TTG AAT TGG TTG ACC CAC TTA AAT TAC AAA TAT CCA GCA TTG AAA GTT ACT ATG CCA AAC AAT GAA AAA TTT GAC AAA TTG TAC ATT TGG GGG GCT CAC CAC CCG GGT ACG TAC AAT GAC CAA ATC AGC CTA TAT GCT CAA GCA TCA GGA ATA ATC ACA GTC TCT ACC AAA AGA ACC CAA CAA ACT GTG ATC CCG AAT ATC GGA TCT AGA CCC AGA GTA AGG GAT ATC CCC AGC AGA ATA AGC ATC TAT TGG ACA ATA GTA AAA CCG GGA GAC ATA CTT TTG ATT AAC AGC ACA GGG AAT CTA ATT GCT CCT CGG GGT TAT TTC AAA TTA CAA AAT GGG AAA AGC TCA ATA ATG AGA TCA GAT GCA CCC ATT GGC AAA TGT AAT TCT GAA TGT ATC ACC CCA AAT GGA AGC ATT CCC AAT GAC AGA CCA TTC CAA AAT GTA AAT AGG ATC ACA TAT GGG ACC TGT CCC AGA TAT GTT AAG CAA AAC ACC CTG AAA TTG GCA ACA GGA ATG AGA AAT GTA CCA GAG AAA CAA ACT AGA GGC ATA TTT GGC GCA ATC GCG GGT TTC ATA GAA AAT GGT TGG GAG GGA ATG GTT GAT GGT TGG TAC GGT TTC AGG CAC CAA AAT TCT GAG GGA ATG GGA CAA GCA GCA GAT CTC AAA AGC ACT CAA GCA GCA ATT AAT CAA ATC AAT GGA AAG CTG AAT AGG TTG ATC GGG AAA ACC AAT GAG AAA TTC CAT CAG ATT GAA AAA GAA TTC TCA GAG GTA GAA GGA AGA ATT CAG GAC CTC GAG AAA TAT GTT GAG GAC ACC AAA ATA GAT CTC TGG TCA TAC AAC GCG GAG CTT CTT GTT GCC CTG GAG AAC CAA CAT ACA ATT GAT CTA ACT GAC TCA GAA ATG AAC AAA CTG TTT GAA AGA ACA AAG AAG CAA CTG AGG GAA AAT GCT GAG GAT ATG GGC AAT GGT TGT TTC AAA ATA TAC CAC AAA TGT GAC AAT GCC TGC ATA GGA TCA ATC AGA AAT GGA ACT TAT GAC CAT GAT GTA TAC AGA GAT GAA GCA TTG AGC AAC CGG TTC CAG ATC AAA GGT GTT GAG CTG AAG GCA GGA TAC AAA GAT TGG ATC CTA TGG ATT TCC TTT GCC ATA TCA TGT TTT TTG CTT TAT GTT GTT TTG TTG GGG TTC ATC ATG TGG GCC TGC CAA AAG GGC AAC ATT AGG TGC AAC ATT TGC ATT 
25
+A/Swine/GD/1599/2012       ATG AAG ACT ATT ATT GCT TTG AGC TAC ATT CTA TGT CTG GTT TTT GCT CAA AAA TTT CCT GGA AAT GAC AAC AAC ATG GCA ATG CTG TGC CTT GGG CAC CAT GCA GTA CCA AAC GGA ACG ATG GTG AAA ACA ATC ACG AAT GAC CAA ATT GAA GTT ACT AAT GCT ACT GAG CTG GTT CAG AGT TCC TCA ACA GGT GGA ATA TGC AAC AGC CCT TAT CAG ATC CTT GAT GGA GGA AAC TGC ACA CTA ATA GAT GCT ATA TTG GGA GAC CCT CAG TGT GAT GGC TTC CAG AAT AAG AAA TGG GAC CTT TTT GTT GAA CGC AGT AAA GCC TAC AGC AAC TGT TAC CCT TAT GAT GTG CCG GAT TAT GCC TCC CTT AGG TCA ATA GTT GCC TCA TCC GGC ACG CTG GAA TTT AAC AGT GAA AGC TTC AAT TGG ACT GGA GTC ACT CAA AAT GGG AAA AGC GCT TCT TGC AAA AGG GGA TCT GAT AAC AGT TTC TTT AGT AGA TTG AAT TGG TTG ACC CAC TTA AAT TAC AAA TAT CCA GCA TTG AAA GTT ACT ATG CCA AAC AAT GAA AAA TTT GAC AAA TTG TAC ATT TGG GGG GCT CAC CAC CCG GGT ACG TAC AAT GAC CAA ATC AGC CTA TAT GCT CAA GCA TCA GGA ATA ATC ACA GTC TCT ACC AAA AGA ACC CAA CAA ACT GTG ATC CCG AAT ATC GGA TCT AGA CCC AGA ATA AGG GAT ATC CCC AGC AGA ATA AGC ATC TAT TGG ACA ATA GTA AAA CCG GGA GAC ATA CTT TTG ATT AAC AGC ACA GGG AAT CTA ATT GCT CCT CGG GGT TAT TTC AAA TTA CAA AAT GGG AAA AGC TCA ATA ATG AGA TCA GAT GCA CCC ATT GGC AAA TGC AAT TCT GAA TGT ATC ACC CCA AAT GGA AGC ATT CCC AAT GAC AGA CCA TTT CAA AAT GTA AAT AGG ATC ACA TAT GGG GCC TGT CCC AGA TAT GTT AAG CAA AAC ACC CTG AAA TTG GCA ACA GGA ATG AGA AAT GTA CCA GAG AAA CAA ACT AGA GGC ATA TTT GGC GCA ATC GCG GGT TTC ATA GAA AAT GGT TGG GAG GGA ATG GTT GAT GGT TGG TAC GGT TTC AGG CAC CAA AAT TCT GAG GGA ATG GGA CAA GCA GCA GAT CTC AAA AGC ACT CAA GCA GCA ATC AAT CAA ATC AAT GGA AAG CTG AAT AGG TTG ATC GGG AAA ACC AAT GAG AAA TTC CAT CAG ATT GAA AAA GAA TTC TCA GAG GTA GAA GGA AGA ATT CAG GAC CTC GAG AAA TAT GTT GAG GAC ACC AAA ATA GAT CTC TGG TCA TAC AAC GCG GAG CTT CTT GTT GCC CTG GAG AAC CAA CAT ACA ATT GAT CTA ACT GAC TCA GAA ATG AAC AAA CTG TTT GAA AGA ACA AGG AAG CAA CTG AGG GAA AAT GCT GAG GAT ATG GGC AAT GGT TGT TTC AAA ATA TAC CAC AAA TGT GAC AAT GCC TGC ATA GGA TCA ATC AGA AAT GGA ACT TAT GAC CAT GAT GTA TAC AGA GAT GAA GCA TTG AGC AAC CGG TTC CAG ATC AAA GGT GTT GAG CTG AAA GCA GGA TAC AAA GAT TGG ATC CTA TGG ATT TCC TTT GCC ATA TCA TGT TTT TTG CTT TGT GTT GTT TTG TTG GGG TTC ATC ATG TGG GCC TGC CAA AAG GGC AAC ATT AGG TGC AAC ATT TGC ATT 
26
+A/Swine/HK/2454/2012       ATG AAG ACT ATC ATT GCT TTG AGC TAC ATT CTA TGT CTG GTT TTC GCT CAA AAA TTT CCT GGA AAT GAC AAC AGC ATG GCA ACG CTG TGC CTT GGG CAC CAT GCA GTA CCA AAC GGA ACG ATG GTG AAA ACA ATA ACG AAT GAC CAA ATT GAA GTC ACT AAT GCT ACT GAG CTG GTT CAG AGT TCC TCA ACA GGT GGA ATA TGC AAC AGC CCT CAT CAG ATC CTT GAT GGA GGA AAC TGC ACA CTA ATA GAT GCT CTA TTG GGA GAC CCT CAG TGT GAT GGC TTC CAG AAT AAG AAA TGG GAC CTT TTT GTT GAA CGC AGC AAA GCC TAC AGC AAC TGT TAC CCT TAT GAT GTG CCG GAT TAT ACA TCC CTT AGG TCA ATA GTT GCT TCA TCC GGC ACA CTG GAA TTT AAC AAT GAA AGC TTC AAT TGG ACT GGA GTC ACT CAA AAT GGA AAA AGC GCT TCG TGC AAA AGA GGA TCT GAC AAC AGT TTC TTT AGT AGA TTG AAT TGG TTG ACC CAC TTA AAT TAC AAA TAT CCA GCA TTG AAA GTT ACT ATG CCA AAC AAT GAA AAA TTT GAC AAA TTG TAC ATT TGG GGG GTC CAC CAC CCG GGC ACG TAC AAT GAC CAA ATC AGC CTA TAT GCT CAA GCA TCA GGA ATA ATC ACA GTC TCT ACC AAA AGA AAC CAA CAA ACT GTG ATC CCA AAT ATC GGA TCT AGA CCC AGA GTA AGG GAT ATC CCC AGC AGA ATA AGC ATC TAT TGG ACA ATA GTA AAA CCA GGA GAC ATA CTT TTG ATT AAC AGC ACA GGG AAT CTA ATT GCT CCT CGG GGT TAC TTC AAA ATA CAA AGT GGG AAA AGC TCA ATA ATG AGA TCA GAT GCA CCC ATT GGC AAA TGC AAT TCT GAA TGT ATC ACT CCA AAT GGA AGC ATT CCC AAT GAC AAA CCA TTT CAA AAT GTA AAT AGA ATC ACA TAT GGG GCC TGT CCC AGG TAT GTT AAG CAA AAC ACC CTA AAA TTG GCA ACA GGA ATG AGA AAT GTT CCA GAG AAA CAA ACT AGA GGC ATA TTT GGC GCA ATC GCG GGT TTC ATA GAA AAT GGT TGG GAG GGA ATG GTT GAT GGT TGG TAC GGT TTC AGG CAT CAA AAT TCT GAG GGA ATG GGA CAA GCA GCA GAT CTC AAA AGC ACT CAA GCA GCG GTC AAT CAA ATC AAT GGA AAG CTG AAT AGG TTG ATC GGG AAA ACC AAT GAG AAA TTC CAT CAG ATT GAA AAA GAA TTC TCA GAG GTA GAA GGG AGA ATT CAG GAC CTC GAG AAA TAT GTT GAG GAC ACC AAA ATA GAT CTC TGG TCA TAC AAC GCG GAG CTT CTT GTT GCC CTG GAG AAC CAA CAT ACA ATT GAT CTA ACT GAC TCA GAA ATG GAC AAA CTG TTT GAA AGA ACA AAG AAG CAA CTG AGG GAA AAT GCT GAG GAT ATG GGC AAT GGT TGT TTC AAA ATA TAC CAC AAA TGT GAC AAT GCC TGC ATA GGA TCA ATC AGA AAT GGA ACT TAT GAC CAT GAT ATA TAC AGA GAT GAA GCA TTG AGC AAC CGG TTC CAG ATC AAA GGT GTT GAG CTG AAG GCA GGA CAC AAA GAT TGG ATC CTA TGG ATT TCC TTT GCC ATA TCA TGT TTT TTG CTT TGT GTT GTT TTG TTG GGG TTC ATC ATG TGG GCC TGC CAA AAG GGC AAC ATT AGG TGC AAC ATT TGC ATT 
27
+A/Swine/GX/508/2012        ATG AAG ACT ATC ATT GCT TTG AGC TAC ATT CTA TGT CTG GTT TTC GCT CAA AAA TTT CCT GGA AAT GAC AAC AAC ATG GCA ATG CTG TGC CTT GGG CAC CAT GCA GTA CCA AAC GGA ACG ATG GTG AAA ACA ATC ACA AAT GAC CAA ATT GAA GTT ACT AAT GCT ACT GAG CTG GTT CAG AGT TCC TCA ACA GGT GGA ATA TGC AAC AGC CCT TAT CAG ATC CTT GAT GGA GGA AAC TGC ACA CTA ATA GAT GCT CTA TTG GGA GAC CCT CAG TGT GAT GGC TTC CAG AAT AAG AAA TGG GAC CTT TTT GTT GAA CGC AGC AAA GCC TAC AGC AAC TGT TAC CCT TAT GAT GTG CCG GAT TAT GCC TCC CTT AGG TCA ATA GTT GCC TCA TCC GGC ACG CTG GAA TTT AAC AAT GAA AGC TTC AAT TGG ACT GGA GTC ACT CAA AAT GGA AAA AGC GCT TCT TGC AAA AGG GGA TCT GAT AAC AGT TTC TTT AGT AGA TTG AAT TGG TTG ACC CAC TTA AAT TAC AAA TAT CCA GCA TTG AAA GTT ACT ATG CCA AAC AAT GAA AAA TTT GAC AAA TTG TAC ATT TGG GGG GCT CAC CAC CCG GGT ACG TAC AAT GAC CAA ATC AGC CTA TAT GCT CAA GCA TCA GGA ATA ATC ACA GTC TCT ACC AAA AGA ACC CAA CAA ACT GTG ATC CCG AAT ATC GGA TCT AGA CCC AGA GTA AGG GAT ATC CCC AGC AGA ATA AGC ATC TAT TGG ACA ATA GTA AAA CCG GGA GAC ATA CTT TTG ATT AAC AGC ACA GGG AAT CTA ATT GCT CCT CGG GGT TAT TTC AAA TTA CAA AAT GGG AAA AGC TCA ATA ATG AGA TCA GAT GCA CCC ATT GGC AAA TGC AAT TCT GAA TGT ATC ACC CCA AAT GGA AGC ATT CCC AAT GAC AGA CCA TTT CAA AAT GTA AAT AGG ATC ACA TAT GGG ACC TGC CCC AGA TAT GTT AAG CAA AAC ACC CTG AAA TTG GCA ACA GGA ATG AGA AAT GTA CCA GAG AAA CAA ACT AGA GGC ATA TTT GGC GCA ATC GCG GGT TTC ATA GAA AAT GGT TGG GAG GGA ATG GTT GAT GGT TGG TAC GGT TTC AGG CAC CAA AAT TCT GAG GGA ATG GGA CAA GCA GCA GAT CTC AAG AGC ACT CAA GCA GCA ATT AAT CAA ATC AAT GGA AAG CTG AAT AGG TTG ATC GGG AAA ACC AAT GAG AAA TTC CAT CAG ATT GAA AAA GAA TTC TCA GAG GTA GAA GGA AGA ATT CAG GAC CTC GAG AAA TAT GTT GAG GAC ACC AAA ATA GAT CTC TGG TCA TAC AAC GCG GAG CTT CTT GTT GCC CTG GAG AAC CAA CAT ACA ATT GAT CTA ACT GAC TCA GAA ATG AAC AAA CTG TTT GAA AGA ACA AAG AAG CAA CTG AGG GAA AAT GCT GAG GAT ATG GGC AAT GGT TGT TTC AAA ATA TAC CAC AAA TGT GAC AAT GCC TGC ATA GGA TCA ATC AGA AAT GGA ACT TAT GAC CAT GAT GTA TAC AGA GAT GAA GCA TTG AGC AAC CGG TTC CAG ATC AAA GGT GTT GAG CTG AAG GCA GGA TAC AAA GAT TGG ATC CTA TGG ATT TCC TTT GCC ACA TCA TGT TTT TTG CTT TGT GTT GTT TTG TTG GGG TTC ATC ATG TGG GCC TGC CAA AAG GGC AAC ATT AGG TGC AAT ATT TGC ATT 
28
+A/Swine/HK_NS1651/2012     ATG AAG ACT ATC ATT GCT TTG AGC TAC ATT CTA TGT CTG GTT CTC GCT CAA AAA TTT CCT GGA AAT GAC AAC AAC AGG GCA ATG CTG TGC CTT GGG CAC CAT GCA GTA CCA AAC GGA ACG ATG GTG AAA ACA ATC ACG AAT GAC CAA ATT GAA GTT ACT AAT GCT ACT GAG CTG GTT CAG AGT TCC TCA ACA GGT GGA ATA TGC AAC AGC CCT TAT CAG ATC CTT GAT GGA GGA AAC TGC ACA CTA ATA GAT GCT CTA TTG GGA GAC CCT CAG TGT GAT GGC TTC CAG AAT AAG AGA TGG GAC CTT TTT GTT GAA CGC AGC AAA GCC TAC AGC AAC TGT TAC CCT TAT GAG GTG CCG GAT TAT GCC TCC CTT AGG TCA ATA GTT GCC TCA TCC GGC ACA CTG GAA TTT AAC AAT GAA AGC TTC AAT TGG ACT GGA GTC ACT CAA AAT GGA AAA AGC GCT TCT TGC AAA AGG GGT TTT GAT AAC AGT TTC TTT AGT AGA TTG AA