Browse code

Update of citations + fix of msaPrettyPrint() function

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/msa@108923 bc3139a8-67e5-0310-9ffc-ced21a209358

Ulrich Bodenhofer authored on 29/09/2015 11:32:18
Showing14 changed files

... ...
@@ -1,8 +1,8 @@
1 1
 Package: msa
2 2
 Type: Package
3 3
 Title: Multiple Sequence Alignment
4
-Version: 1.0.1
5
-Date: 2015-06-12
4
+Version: 1.0.2
5
+Date: 2015-09-29
6 6
 Author: Enrico Bonatesta, Christoph Horejs-Kainrath, Ulrich Bodenhofer
7 7
 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
8 8
 Description: This package provides a unified R/Bioconductor interface to the
... ...
@@ -57,24 +57,24 @@ msaPrettyPrint <- function(x, y, output=c("pdf", "tex", "dvi", "asis"),
57 57
         stop("The parameter alFile has an invalid argument!")
58 58
 
59 59
     if (!is(x, "MultipleAlignment"))
60
-        stop("The parameter x has an invalid argument! \n", 
60
+        stop("The parameter x has an invalid argument! \n",
61 61
              "x must be a multiple alignment object!")
62
-    
62
+
63 63
 
64 64
     if (output != "asis")
65 65
     {
66 66
         if (!is.numeric(paperWidth) || length(paperWidth) != 1 ||
67 67
             paperWidth <= 0)
68
-            stop("The parameter paperWidth must be ", 
68
+            stop("The parameter paperWidth must be ",
69 69
                  "single positive number (unit: inches)!")
70 70
 
71 71
         if (!is.numeric(paperHeight) || length(paperHeight) != 1 ||
72 72
             paperHeight <= 0)
73
-            stop("The parameter paperHeight must be ", 
73
+            stop("The parameter paperHeight must be ",
74 74
                  "single positive number (unit: inches)!")
75 75
 
76 76
         if (!is.numeric(margins) || length(margins) != 2)
77
-            stop("The parameter margins must be ", 
77
+            stop("The parameter margins must be ",
78 78
                  "two positive numbers (unit: inches)!")
79 79
     }
80 80
 
... ...
@@ -85,14 +85,14 @@ msaPrettyPrint <- function(x, y, output=c("pdf", "tex", "dvi", "asis"),
85 85
             if (max(subset) < .Machine$integer.max)
86 86
                 subset <- as.integer(subset)
87 87
             else
88
-               stop("One or more values for parameter subset ", 
88
+               stop("One or more values for parameter subset ",
89 89
                     "are larger than integer!")
90 90
         }
91 91
         else if (!is.integer(subset))
92 92
             stop("The parameter subset has an invalid argument!")
93 93
 
94 94
         if (length(subset) < 2)
95
-            stop("The parameter subset is expected to be \n", 
95
+            stop("The parameter subset is expected to be \n",
96 96
                  " a vector with at least 2 entries!")
97 97
 
98 98
         if (!all(subset %in% 1:nrow(x)))
... ...
@@ -122,7 +122,7 @@ msaPrettyPrint <- function(x, y, output=c("pdf", "tex", "dvi", "asis"),
122 122
 
123 123
     if (!is.numeric(consensusThreshold) || length(consensusThreshold) != 1 ||
124 124
         consensusThreshold < 0 || consensusThreshold > 100)
125
-        stop("The parameter consensusThreshold must be \n", 
125
+        stop("The parameter consensusThreshold must be \n",
126 126
              "a single numeric between 0 and 100 !")
127 127
 
128 128
     if (shadingMode %in% c("identical", "similar"))
... ...
@@ -151,9 +151,9 @@ msaPrettyPrint <- function(x, y, output=c("pdf", "tex", "dvi", "asis"),
151 151
                                          "accessible area"))
152 152
         else
153 153
             stop("Missing shadingModeArg for functional shading mode. \n",
154
-                 "Valid values are: \n", 
155
-                 "\"charge\", \n", 
156
-                 "\"hydropathy\", \n", 
154
+                 "Valid values are: \n",
155
+                 "\"charge\", \n",
156
+                 "\"hydropathy\", \n",
157 157
                  "\"structure\", \n",
158 158
                  "\"chemical\",\n",
159 159
                  " \"rasmol\",\n",
... ...
@@ -203,7 +203,7 @@ msaPrettyPrint <- function(x, y, output=c("pdf", "tex", "dvi", "asis"),
203 203
     if (output != "asis")
204 204
     {
205 205
         if (!is.character(file) || length(file) > 1)
206
-            stop("The argument for parameter file must be \n", 
206
+            stop("The argument for parameter file must be \n",
207 207
                  "a single character string!")
208 208
 
209 209
         if (substr(file, nchar(file) - 2, nchar(file)) != output)
... ...
@@ -241,6 +241,11 @@ msaPrettyPrint <- function(x, y, output=c("pdf", "tex", "dvi", "asis"),
241 241
 
242 242
     texOutput <- paste0("\\begin{texshade}{", stratifyFilenames(alFile), "}")
243 243
 
244
+    if (is(x, "AAMultipleAlignment"))
245
+        texOutput <- c(texOutput, "\\seqtype{P}")
246
+    else
247
+        texOutput <- c(texOutput, "\\seqtype{N}")
248
+
244 249
     if (length(toShow) == 1)
245 250
     {
246 251
         if (sum(width(toShow)) < ncol(x))
... ...
@@ -1,7 +1,7 @@
1 1
 ##345678901234567890123456789012345678901234567890123456789012345678901234567890
2 2
 citHeader("To cite package 'msa' in publications use:")
3 3
 
4
-#year <- sub(".*(2[[:digit:]]{3})-.*", "\\1", meta$Date, perl = TRUE) 
4
+#year <- sub(".*(2[[:digit:]]{3})-.*", "\\1", meta$Date, perl = TRUE)
5 5
 #vers <- paste("R package version", meta$Version)
6 6
 desc <- packageDescription("msa")
7 7
 year <- sub(".*(2[[:digit:]]{3})-.*", "\\1", desc$Date)
... ...
@@ -9,19 +9,21 @@ vers <- paste("R package version", desc$Version)
9 9
 url  <- desc$URL
10 10
 
11 11
 
12
-citEntry(entry="Manual", 
13
-         title = "msa -- An R Package for Multiple Sequence Alignment.", 
14
-         author = personList(as.person("Enrico Bonatesta"), as.person("Christoph Horejs-Kainrath"), as.person("Ulrich Bodenhofer")),
15
-         year = year, 
16
-         note = vers,
17
-         organization=paste("Institute of Bioinformatics",
18
-                            "Johannes Kepler University", sep=", "),
19
-         address="Linz, Austria",
20
-         url=url,
21
-         textVersion = 
22
-             paste("Enrico Bonatesta, Christoph Horejs-Kainrath and Ulrich Bodenhofer (", year, "). ",
23
-                   "msa -- An R Package for Multiple Sequence Alignment. ",
24
-                   vers, ".", sep="")
12
+citEntry(entry="Article",
13
+         title = "msa: an R package for multiple sequence alignment",
14
+         author = personList(as.person("Ulrich Bodenhofer"),
15
+                             as.person("Enrico Bonatesta"),
16
+                             as.person("Christoph Horejs-Kainrath"),
17
+                             as.person("Sepp Hochreiter")),
18
+         journal="Bioinformatics",
19
+         note="(accepted)",
20
+         year="2015",
21
+         doi="10.1093/bioinformatics/btv494",
22
+         textVersion =
23
+             paste("U. Bodenhofer, E. Bonatesta, C. Horejs-Kainrath, and S. Hochreiter (2015)",
24
+                   "msa: an R package for multiple sequence alignment.",
25
+                   "Bioinformatics (accepted).",
26
+                   "DOI: 10.1093/bioinformatics/btv176.")
25 27
 )
26 28
 
27 29
 citFooter(
... ...
@@ -1,6 +1,10 @@
1 1
 Change history of package msa:
2 2
 ==============================
3 3
 
4
+Version 1.0.2:
5
+- fix of improperly aligned sequence logos produced by msaPrettyPrint()
6
+- updated citation information
7
+
4 8
 Version 1.0.1:
5 9
 - fix of msa() function
6 10
 
... ...
@@ -37,6 +37,14 @@ The following slots are defined for \code{MsaMetaData} objects:
37 37
 \author{Enrico Bonatesta and Christoph Horejs-Kainrath
38 38
   <msa@bioinf.jku.at>
39 39
 }
40
+\references{
41
+  \url{http://www.bioinf.jku.at/software/msa}
42
+  
43
+  U. Bodenhofer, E. Bonatesta, C. Horejs-Kainrath, and S. Hochreiter
44
+  (2015). msa: an R package for multiple sequence alignment. 
45
+  \emph{Bioinformatics} (accepted). DOI:
46
+  \href{http://dx.doi.org/10.1093/bioinformatics/btv494}{10.1093/bioinformatics/btv494}.
47
+}
40 48
 \seealso{\code{\link{msa}}, \code{\link{msaClustalW}},
41 49
   \code{\link{msaClustalOmega}}, \code{\link{msaMuscle}},
42 50
   \code{\linkS4class{MsaAAMultipleAlignment}},
... ...
@@ -81,6 +81,14 @@
81 81
 \author{Enrico Bonatesta and Christoph Horejs-Kainrath
82 82
   <msa@bioinf.jku.at>
83 83
 }
84
+\references{
85
+  \url{http://www.bioinf.jku.at/software/msa}
86
+  
87
+  U. Bodenhofer, E. Bonatesta, C. Horejs-Kainrath, and S. Hochreiter
88
+  (2015). msa: an R package for multiple sequence alignment. 
89
+  \emph{Bioinformatics} (accepted). DOI:
90
+  \href{http://dx.doi.org/10.1093/bioinformatics/btv494}{10.1093/bioinformatics/btv494}.
91
+}
84 92
 \seealso{\code{\link{msa}}, \code{\link{msaClustalW}},
85 93
   \code{\link{msaClustalOmega}}, \code{\link{msaMuscle}},
86 94
   \code{\linkS4class{MsaMetaData}}
... ...
@@ -27,6 +27,11 @@
27 27
 }
28 28
 \references{
29 29
   \url{http://www.bioinf.jku.at/software/msa}
30
+  
31
+  U. Bodenhofer, E. Bonatesta, C. Horejs-Kainrath, and S. Hochreiter
32
+  (2015). msa: an R package for multiple sequence alignment. 
33
+  \emph{Bioinformatics} (accepted). DOI:
34
+  \href{http://dx.doi.org/10.1093/bioinformatics/btv494}{10.1093/bioinformatics/btv494}.
30 35
 
31 36
   Thompson, J. D., Higgins, D. G., and Gibson, T. J. (1994)
32 37
   CLUSTAL W: improving the sensitivity of progressive multiple sequence
... ...
@@ -132,6 +132,11 @@
132 132
 \references{
133 133
   \url{http://www.bioinf.jku.at/software/msa}
134 134
   
135
+  U. Bodenhofer, E. Bonatesta, C. Horejs-Kainrath, and S. Hochreiter
136
+  (2015). msa: an R package for multiple sequence alignment. 
137
+  \emph{Bioinformatics} (accepted). DOI:
138
+  \href{http://dx.doi.org/10.1093/bioinformatics/btv494}{10.1093/bioinformatics/btv494}.
139
+ 
135 140
   \url{http://www.clustal.org/download/clustalw_help.txt}
136 141
 
137 142
   \url{http://www.clustal.org/omega/README}
... ...
@@ -76,6 +76,11 @@
76 76
 }
77 77
 \references{
78 78
   \url{http://www.bioinf.jku.at/software/msa}
79
+  
80
+  U. Bodenhofer, E. Bonatesta, C. Horejs-Kainrath, and S. Hochreiter
81
+  (2015). msa: an R package for multiple sequence alignment. 
82
+  \emph{Bioinformatics} (accepted). DOI:
83
+  \href{http://dx.doi.org/10.1093/bioinformatics/btv494}{10.1093/bioinformatics/btv494}.
79 84
 
80 85
   \url{http://www.clustal.org/omega/README}
81 86
   
... ...
@@ -79,7 +79,12 @@
79 79
 }
80 80
 \references{
81 81
   \url{http://www.bioinf.jku.at/software/msa}
82
-  
82
+   
83
+  U. Bodenhofer, E. Bonatesta, C. Horejs-Kainrath, and S. Hochreiter
84
+  (2015). msa: an R package for multiple sequence alignment. 
85
+  \emph{Bioinformatics} (accepted). DOI:
86
+  \href{http://dx.doi.org/10.1093/bioinformatics/btv494}{10.1093/bioinformatics/btv494}.
87
+ 
83 88
   \url{http://www.clustal.org/download/clustalw_help.txt}
84 89
 
85 90
   Thompson, J. D., Higgins, D. G., and Gibson, T. J. (1994)
... ...
@@ -85,6 +85,11 @@
85 85
 }
86 86
 \references{
87 87
   \url{http://www.bioinf.jku.at/software/msa}
88
+  
89
+  U. Bodenhofer, E. Bonatesta, C. Horejs-Kainrath, and S. Hochreiter
90
+  (2015). msa: an R package for multiple sequence alignment. 
91
+  \emph{Bioinformatics} (accepted). DOI:
92
+  \href{http://dx.doi.org/10.1093/bioinformatics/btv494}{10.1093/bioinformatics/btv494}.
88 93
 
89 94
   \url{http://www.drive5.com/muscle/muscle.html}
90 95
   
... ...
@@ -188,9 +188,14 @@
188 188
   <msa@bioinf.jku.at>
189 189
 }
190 190
 \references{
191
-\url{http://www.bioinf.jku.at/software/msa}
191
+  \url{http://www.bioinf.jku.at/software/msa}
192
+  
193
+  U. Bodenhofer, E. Bonatesta, C. Horejs-Kainrath, and S. Hochreiter
194
+  (2015). msa: an R package for multiple sequence alignment. 
195
+  \emph{Bioinformatics} (accepted). DOI:
196
+  \href{http://dx.doi.org/10.1093/bioinformatics/btv494}{10.1093/bioinformatics/btv494}.
192 197
 
193
-\url{https://www.ctan.org/pkg/texshade}
198
+  \url{https://www.ctan.org/pkg/texshade}
194 199
 
195 200
   Beitz, E. (2000) TeXshade: shading and labeling of multiple
196 201
   sequence alignments using LaTeX2e
... ...
@@ -9,6 +9,38 @@
9 9
   pages =	 {135--139}
10 10
 }
11 11
 
12
+@article{Bodenhofer2015,
13
+  author =	 {U. Bodenhofer and E. Bonatesta and
14
+                  C. Horej\v{s}-Kainrath and S. Hochreiter},
15
+  title =	 {{msa}: an {R} package for multiple sequence
16
+                  alignment},
17
+  journal =	 {Bioinformatics},
18
+  year =	 2015,
19
+  note =	 {(accepted)}
20
+}
21
+
22
+@article{Brudno2003,
23
+  author =	 {M. Brudno and M. Chapman and B. G\"ottgens and
24
+                  S. Batzoglou and B. Morgenstern},
25
+  title =	 {Fast and sensitive multiple alignment of large
26
+                  genomic sequences},
27
+  journal =	 {BMC Bioinformatics},
28
+  year =	 2003,
29
+  volume =	 4,
30
+  pages =	 66
31
+}
32
+
33
+@article{Dagum1998,
34
+  author =	 {L. Dagum and R. Menon},
35
+  title =	 {{OpenMP}: an industry standard {API} for
36
+                  shared-memory programming},
37
+  journal =	 {Computational Science \&\ Engineering, IEEE},
38
+  volume =	 5,
39
+  number =	 1,
40
+  pages =	 {46--55},
41
+  year =	 1998
42
+}
43
+
12 44
 @article{Eddelbuettel2011,
13 45
   title =	 {{Rcpp}: Seamless {R} and {C++} Integration},
14 46
   author =	 {D. Eddelbuettel and R. Fran\c{c}ois},
... ...
@@ -49,6 +81,16 @@
49 81
   year =	 2004
50 82
 }
51 83
 
84
+@article{Edgar2006,
85
+  author =	 {R. C. Edgar and S. Batzoglou},
86
+  title =	 {Multiple sequence alignment},
87
+  journal =	 {Curr. Opin. Struct. Biol.},
88
+  volume =	 16,
89
+  number =	 3,
90
+  pages =	 {368--373},
91
+  year =	 2006
92
+}
93
+
52 94
 @book{Lamport1999,
53 95
   title =	 {{\LaTeX} --- A Document Preparation System. User's
54 96
                   Guide and Reference Manual},
... ...
@@ -58,6 +100,20 @@
58 100
   year =	 1999
59 101
 }
60 102
 
103
+@article{Larkin2007,
104
+  author =	 {M. A. Larkin and G. Blackshields and N. P. Brown and
105
+                  R. Chenna and P. A. McGettigan and H. McWilliam and
106
+                  F. Valentin and I. M. Wallace and A. Wilm and
107
+                  R. Lopez and J. D. Thompson and T. J. Gibson and
108
+                  D. G. Higgins},
109
+  title =	 {{Clustal W} and {Clustal X} version 2.0},
110
+  journal =	 {Bioinformatics},
111
+  year =	 2007,
112
+  volume =	 23,
113
+  number =	 21,
114
+  pages =	 {2947--2948}
115
+}
116
+
61 117
 @inproceedings{Leisch2002,
62 118
   author =	 {F. Leisch},
63 119
   title =	 {Sweave: dynamic generation of statistical reports
... ...
@@ -71,6 +127,17 @@
71 127
   year =	 2002
72 128
 }
73 129
 
130
+@article{Loytynoja2012,
131
+  author =	 {A. L\"oytynoja and A. J. Vilella and N. Goldman},
132
+  title =	 {Accurate extension of multiple sequence alignments
133
+                  using a phylogeny-aware graph algorithm},
134
+  journal =	 {Bioinformatics},
135
+  year =	 2012,
136
+  volume =	 28,
137
+  number =	 13,
138
+  pages =	 {1684--1691}
139
+}
140
+
74 141
 @article{Morgenstern1999,
75 142
   author =	 {B. Morgenstern},
76 143
   title =	 {{DIALIGN 2}: improvement of the segment-to-segment
... ...
@@ -103,6 +170,26 @@
103 170
   pages =	 {205--217}
104 171
 }
105 172
 
173
+@article{Notredame2007,
174
+  author =	 {C. Notredame},
175
+  title =	 {Recent Evolutions of Multiple Sequence Alignment
176
+                  Algorithms},
177
+  journal =	 {PLoS Comput. Biol.},
178
+  year =	 2007,
179
+  volume =	 3,
180
+  number =	 8,
181
+  pages =	 {e123}
182
+}
183
+
184
+@manual{Pages2015,
185
+  title =	 {Biostrings: String objects representing biological
186
+                  sequences, and matching algorithms},
187
+  author =	 {H. Pag\`es and P. Aboyoun and R. Gentleman and
188
+                  S. DebRoy},
189
+  note =	 {R package version 2.36.1},
190
+  year =	 2015
191
+}
192
+
106 193
 @article{Sievers2011,
107 194
   author =	 {F. Sievers and A. Wilm and D. Dineen and
108 195
                   T. J. Gibson and K. Karplus and W. Li and R. Lopez
... ...
@@ -116,6 +203,16 @@
116 203
   year =	 2011
117 204
 }
118 205
 
206
+@article{Szalkowski2012,
207
+  author =	 {A. M. Szalkowski},
208
+  title =	 {Fast and robust multiple sequence alignment with
209
+                  phylogeny-aware gap placement},
210
+  journal =	 {BMC Bioinformatics},
211
+  year =	 2012,
212
+  volume =	 13,
213
+  pages =	 129
214
+}
215
+
119 216
 @article{Thompson1994,
120 217
   author =	 {J. D. Thompson and D. G. Higgins and T. J. Gibson},
121 218
   title =	 {{CLUSTAL W}: improving the sensitivity of
... ...
@@ -129,6 +226,16 @@
129 226
   pages =	 {4673--4680}
130 227
 }
131 228
 
229
+@article{Wallace2005,
230
+  author =	 {I. M. Wallace and G. Blackshields and D. G. Higgins},
231
+  title =	 {Multiple sequence alignments},
232
+  journal =	 {Curr. Opin. Struct. Biol.},
233
+  volume =	 15,
234
+  number =	 3,
235
+  pages =	 {261--266},
236
+  year =	 2005
237
+}
238
+
132 239
 @book{Xie2014,
133 240
   title =	 {Dynamic Documents with R and knitr},
134 241
   author =	 {Y. Xie},
... ...
@@ -83,15 +83,16 @@ first have to read introductory literature on the subjects mentioned above.
83 83
 
84 84
 \section{Introduction}
85 85
 Multiple sequence alignment is one of the most fundamental tasks in
86
-bioinformatics. Algorithms like ClustalW~\cite{Thompson1994},
86
+bioinformatics. Algorithms like ClustalW~\cite{Thompson1994,Larkin2007},
87 87
 ClustalOmega~\cite{Sievers2011}, and MUSCLE~\cite{Edgar2004b,Edgar2004a}
88
-are well known and
89
-widely used. However, all these algorithms are implemented as stand-alone
88
+are well known and widely used (for more comprehensive overviews of methods,
89
+see \cite{Edgar2006,Notredame2007,Wallace2005}).
90
+However, all these algorithms are implemented as stand-alone
90 91
 commmand line programs without any integration into the R/Bioconductor
91 92
 ecosystem. Before the \MSA\ package, only the \verb+muscle+ package has
92 93
 been available in \R, but no other multiple sequence alignment algorithm,
93 94
 although the \verb+Biostrings+ package has provided data types for
94
-representing multiple sequence alignments for quite some time.
95
+representing multiple sequence alignments for quite some time \cite{Pages2015}.
95 96
 The \MSA\ package aims to close that gap by
96 97
 providing a unified R interface to the multiple sequence alignment algorithms
97 98
 ClustalW, ClustalOmega, and MUSCLE. The package requires no additional
... ...
@@ -541,12 +542,6 @@ has a minor memory leak, but the loss of data is so small that no major
541 542
 problems are to be expected except for thousands of executions of
542 543
 ClustalOmega.
543 544
 
544
-\subsubsection*{\shade: Alignment of Sequence Logos}
545
-
546
-\shade\ has some issues with aligning the sequence logo to the multiple
547
-sequence alignment. Under which conditions this happens, would require a
548
-more detailed investigation.
549
-
550 545
 \subsubsection*{ClustalOmega vs.\ Older GCC Versions on Linux/Unix}
551 546
 
552 547
 We have encountered peculiar behavior of ClustalOmega if the package was
... ...
@@ -562,7 +557,7 @@ to update to a newer GCC version and re-install the package.
562 557
 \subsubsection*{ClustalOmega: OpenMP Support on Mac OS}
563 558
 
564 559
 ClustalOmega is implemented to make use of OpenMP (if available on the
565
-target platform). Due to issues on one of the Bioconductor build servers
560
+target platform) \cite{Dagum1998}. Due to issues on one of the Bioconductor build servers
566 561
 running Mac OS, we had to deactivate OpenMP generally for Mac OS platforms.
567 562
 If a Mac OS user wants to re-activate OpenMP, he/she should download the
568 563
 source package tarball, untar it, comment/uncomment the corresponding line in
... ...
@@ -580,7 +575,8 @@ function. This interface will be improved in future versions.
580 575
 We envision the following changes/extensions in future versions of the package:
581 576
 \begin{itemize}
582 577
   \item Integration of more multiple sequence alignment algorithms, such as,
583
-    T-Coffee \cite{Notredame2000} or DIALIGN \cite{Morgenstern1999}
578
+    T-Coffee \cite{Notredame2000} or others
579
+    \cite{Brudno2003,Loytynoja2012,Morgenstern1999,Szalkowski2012}
584 580
   \item Support for retrieving guide trees from the multiple sequence
585 581
     alignment algorithms
586 582
   \item Interface to methods computing phylogenetic trees (e.g.\ as
... ...
@@ -595,10 +591,12 @@ We envision the following changes/extensions in future versions of the package:
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 \section{How to Cite This Package}
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597 593
 If you use this package for research that is published later, you are kindly
598
-asked to cite it as follows:
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+asked to cite it as follows \cite{Bodenhofer2015}:
599 595
 \begin{quotation}
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-\noindent E.~Bonatesta, C.~Horejs-Kainrath, and U.~Bodenhofer, (2015).
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-msa: An R Package for Multiple Sequence Alignment.
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+\noindent U.~Bodenhofer, E.~Bonatesta, C.~Horej\v{s}-Kainrath, and Sepp Hochreiter(2015).
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+msa: an R Package for multiple sequence alignment.
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+{\em Bioinformatics} (accepted). DOI:
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+\href{http://dx.doi.org/10.1093/bioinformatics/btv494}{10.1093/bioinformatics/btv494}.
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 \end{quotation}
603 601
 To obtain a Bib\TeX\ entries of the reference, enter the
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 following into your R session:
... ...
@@ -613,6 +611,11 @@ bibliography below).
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 \section{Change Log}
614 612
 
615 613
 \begin{description}
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+\item[Version 1.0.2:] \mbox{ } \newline
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+  \begin{itemize}
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+    \item fix of improperly aligned sequence logos produced by \verb+msaPrettyPrint()+
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+    \item updated citation information
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+  \end{itemize}
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 \item[Version 1.0.1:] fix of \verb+msa()+ function
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 \item[Version 1.0.0:] first official release as part of Bioconductor 3.1
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 \end{description}
... ...
@@ -628,6 +631,22 @@ E.~Beitz.
628 631
   using {\LaTeX2e}.
629 632
 \newblock {\em Bioinformatics}, 16(2):135--139, 2000.
630 633
 
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+\bibitem{Bodenhofer2015}
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+U.~Bodenhofer, E.~Bonatesta, C.~Horej\v{s}-Kainrath, and S.~Hochreiter.
636
+\newblock {msa}: an {R} package for multiple sequence alignment.
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+\newblock {\em Bioinformatics}, 2015.
638
+\newblock (accepted).
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+
640
+\bibitem{Brudno2003}
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+M.~Brudno, M.~Chapman, B.~G\"ottgens, S.~Batzoglou, and B.~Morgenstern.
642
+\newblock Fast and sensitive multiple alignment of large genomic sequences.
643
+\newblock {\em BMC Bioinformatics}, 4:66, 2003.
644
+
645
+\bibitem{Dagum1998}
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+L.~Dagum and R.~Menon.
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+\newblock {OpenMP}: an industry standard {API} for shared-memory programming.
648
+\newblock {\em Computational Science \&\ Engineering, IEEE}, 5(1):46--55, 1998.
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+
631 650
 \bibitem{Edgar2004b}
632 651
 R.~C. Edgar.
633 652
 \newblock {MUSCLE}: a multiple sequence alignment method with reduced time and
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@@ -640,12 +659,24 @@ R.~C. Edgar.
640 659
   throughput.
641 660
 \newblock {\em Nucleic Acids Res.}, 32(5):1792--1797, 2004.
642 661
 
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+\bibitem{Edgar2006}
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+R.~C. Edgar and S.~Batzoglou.
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+\newblock Multiple sequence alignment.
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+\newblock {\em Curr. Opin. Struct. Biol.}, 16(3):368--373, 2006.
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+
643 667
 \bibitem{Lamport1999}
644 668
 L.~Lamport.
645 669
 \newblock {\em {\LaTeX} --- A Document Preparation System. User's Guide and
646 670
   Reference Manual}.
647 671
 \newblock Addison-Wesley Longman, Amsterdam, 1999.
648 672
 
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+\bibitem{Larkin2007}
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+M.~A. Larkin, G.~Blackshields, N.~P. Brown, R.~Chenna, P.~A. McGettigan,
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+  H.~McWilliam, F.~Valentin, I.~M. Wallace, A.~Wilm, R.~Lopez, J.~D. Thompson,
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+  T.~J. Gibson, and D.~G. Higgins.
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+\newblock {Clustal W} and {Clustal X} version 2.0.
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+\newblock {\em Bioinformatics}, 23(21):2947--2948, 2007.
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+
649 680
 \bibitem{Leisch2002}
650 681
 F.~Leisch.
651 682
 \newblock Sweave: dynamic generation of statistical reports using literate data
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@@ -654,6 +685,12 @@ F.~Leisch.
654 685
   Proceedings in Computational Statistics}, pages 575--580, Heidelberg, 2002.
655 686
   Physica-Verlag.
656 687
 
688
+\bibitem{Loytynoja2012}
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+A.~L\"oytynoja, A.~J. Vilella, and N.~Goldman.
690
+\newblock Accurate extension of multiple sequence alignments using a
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+  phylogeny-aware graph algorithm.
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+\newblock {\em Bioinformatics}, 28(13):1684--1691, 2012.
693
+
657 694
 \bibitem{Morgenstern1999}
658 695
 B.~Morgenstern.
659 696
 \newblock {DIALIGN 2}: improvement of the segment-to-segment approach to
... ...
@@ -666,12 +703,23 @@ N.~Nethercote and J.~Seward.
666 703
 \newblock In {\em Proc. of the ACM SIGPLAN 2007 Conf. on Programming Language
667 704
   Design and Implementation}, San Diego, CA, 2007.
668 705
 
706
+\bibitem{Notredame2007}
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+C.~Notredame.
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+\newblock Recent evolutions of multiple sequence alignment algorithms.
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+\newblock {\em PLoS Comput. Biol.}, 3(8):e123, 2007.
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+
669 711
 \bibitem{Notredame2000}
670 712
 C.~Notredame, D.~G. Higgins, and J.~Heringa.
671 713
 \newblock {T-Coffee}: A novel method for fast and accurate multiple sequence
672 714
   alignment.
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 \newblock {\em J. Mol. Biol.}, 302(1):205--217, 2000.
674 716
 
717
+\bibitem{Pages2015}
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+H.~Pag\`es, P.~Aboyoun, R.~Gentleman, and S.~DebRoy.
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+\newblock {\em Biostrings: String objects representing biological sequences,
720
+  and matching algorithms}, 2015.
721
+\newblock R package version 2.36.1.
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+
675 723
 \bibitem{Sievers2011}
676 724
 F.~Sievers, A.~Wilm, D.~Dineen, T.~J. Gibson, K.~Karplus, W.~Li, R.~Lopez,
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   H.~McWilliam, M.~Remmert, J.~S\"oding, J.~D. Thompson, and D.~G. Higgins.
... ...
@@ -679,6 +727,12 @@ F.~Sievers, A.~Wilm, D.~Dineen, T.~J. Gibson, K.~Karplus, W.~Li, R.~Lopez,
679 727
   alignments using {Clustal Omega}.
680 728
 \newblock {\em Mol. Syst. Biol.}, 7:539, 2011.
681 729
 
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+\bibitem{Szalkowski2012}
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+A.~M. Szalkowski.
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+\newblock Fast and robust multiple sequence alignment with phylogeny-aware gap
733
+  placement.
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+\newblock {\em BMC Bioinformatics}, 13:129, 2012.
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+
682 736
 \bibitem{Thompson1994}
683 737
 J.~D. Thompson, D.~G. Higgins, and T.~J. Gibson.
684 738
 \newblock {CLUSTAL W}: improving the sensitivity of progressive multiple
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@@ -686,6 +740,11 @@ J.~D. Thompson, D.~G. Higgins, and T.~J. Gibson.
686 740
   penalties and weight matrix choice.
687 741
 \newblock {\em Nucleic Acids Res.}, 22(22):4673--4680, 2004.
688 742
 
743
+\bibitem{Wallace2005}
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+I.~M. Wallace, G.~Blackshields, and D.~G. Higgins.
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+\newblock Multiple sequence alignments.
746
+\newblock {\em Curr. Opin. Struct. Biol.}, 15(3):261--266, 2005.
747
+
689 748
 \bibitem{Xie2014}
690 749
 Y.~Xie.
691 750
 \newblock {\em Dynamic Documents with R and knitr}.