@@ -1,8 +1,8 @@

 Package: msa

 Type: Package

 Title: Multiple Sequence Alignment

-Version: 0.99.5

-Date: 2015-04-12

+Version: 0.99.6

+Date: 2015-04-15

 Author: Enrico Bonatesta, Christoph Horejs-Kainrath, Ulrich Bodenhofer

 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>

 Description: This package provides a unified R/Bioconductor interface to the

@@ -17,15 +17,18 @@ URL: http://www.bioinf.jku.at/software/msa/

 License: GPL (>= 2)

 Copyright: See file inst/COPYRIGHT

 Depends: R (>= 3.1.0), methods, Biostrings (>= 2.30.0)

-Imports: Rcpp (>= 0.11.1), BiocGenerics, IRanges (>= 1.20.0), S4Vectors,

-	 tools

+Imports: Rcpp (>= 0.11.1), BiocGenerics, IRanges (>= 1.20.0),

+        S4Vectors, tools

 Suggests: Biobase, knitr

 LinkingTo: Rcpp

-SystemRequirements: GNU make

+SystemRequirements:

 VignetteBuilder: knitr

 LazyLoad: yes

-Collate: AllClasses.R AllGenerics.R params-methods.R version-methods.R 

-         helperFunctions.R inputChecks.R convertRows.R msaPrettyPrint.R

-	 print-methods.R show-methods.R msa.R msaMuscle.R msaClustalW.R 

-         msaClustalOmega.R

-biocViews: MultipleSequenceAlignment, Alignment, MultipleComparison, Sequencing

+Collate: AllClasses.R AllGenerics.R params-methods.R version-methods.R

+        helperFunctions.R inputChecks.R convertRows.R msaPrettyPrint.R

+        print-methods.R show-methods.R msa.R msaMuscle.R msaClustalW.R

+        msaClustalOmega.R

+biocViews: MultipleSequenceAlignment, Alignment, MultipleComparison,

+        Sequencing

+NeedsCompilation: yes

+Packaged: 2015-04-15 13:16:43 UTC; bodenhof

@@ -4,7 +4,7 @@ convertAlnRows <- function(rows, type)

     if (length(rows) < 3 ||

         ##!identical(grep("^CLUSTAL", rows[1L]), 1L) ||

-        !identical(rows[2:3], c("","")))

+        !identical(sub("^\\s+$", "", rows[2:3]), c("", "")))

         stop("There is an invalid aln file!")

     rows <- tail(rows, -3)

@@ -43,7 +43,7 @@ getParamsList <-function(type,

 ##function, which tests a given input sequence

 ##whether it is a character string, or a XStringSet

-transformInputSeq <- function(inputSeq, isFile=FALSE) {

+transformInputSeq <- function(inputSeq) {

     if (!is(inputSeq, "character")) {

         if (is(inputSeq, "XStringSet")) {

             inputSeq <- as.character(inputSeq)

@@ -53,24 +53,6 @@ transformInputSeq <- function(inputSeq, isFile=FALSE) {

         }

     }

-    if (!isFile)

-    {

-        if (is.null(names(inputSeq))) {

-            warning("The input sequences are unnamed! \n",

-                    "Note that the order of sequences \n",

-                    "in the resulting multiple sequence alignment \n",

-                    "may not be preserved, so unique sequence names\n",

-                    "are necessary to recover the order!")

-        }

-        else if (length(unique(names(inputSeq))) != length(inputSeq)){

-            warning("The input sequences are not unique! \n",

-                    "Note that the order of sequences \n",

-                    "in the resulting multiple sequence alignment \n",

-                    "may not be preserved, so unique sequence names \n",

-                    "are necessary to recover the order!")

-        }

-    }

-

     return(inputSeq)

 }

@@ -72,9 +72,8 @@ checkType <- function(type, inputSeqs, msaName){

 ###############################################################################

 ##function, that tests the input of gapOpening.

-##If the value is negative, everything is ok and the function returns

-##the gapOpening parameter. If the input is positive, the value is transformed

-##and a warning is given. If the input is not numeric, an exception is thrown.

+##If the value is numeric, everything is ok and the function returns

+##the gapOpening parameter. If the input is not numeric, an exception is thrown.

 ##Same for missing substitutionMatrix

 checkGapOpening <- function(gapOpening, type, substitutionMatrix,

         defaultDNAValue,  defaultAAValue){

@@ -90,25 +89,18 @@ checkGapOpening <- function(gapOpening, type, substitutionMatrix,

     if (is.numeric(gapOpening)) {

         if (is.matrix(gapOpening)) {

             stop("The parameter gapOpening should be \n",

-                 "a negative numeric, not a matrix!")

+                 "a numeric, not a matrix!")

         }

         if (length(gapOpening) != 1) {

             stop("The parameter gapOpening should be \n",

-                 "a negative numeric, not a vector!")

+                 "a numeric, not a vector!")

         }

         if (is.nan(gapOpening)) {

             stop("The parameter gapOpening should be \n",

-                 "a negative numeric, not a NaN!")

-        }

-        ##check if gapOpening is positive

-        if (gapOpening > 0) {

-            warning("According to BioStrings, the parameter gapOpening \n",

-                    "should be negative! The value is transformed \n",

-                    "to a negative numeric!")

-            gapOpening <- gapOpening * -1;

+                 "a numeric, not a NaN!")

         }

     } else {

-        stop("The parameter gapOpening should be a negative numeric!")

+        stop("The parameter gapOpening should be a numeric!")

     }

     return(gapOpening)

 }

@@ -117,9 +109,8 @@ checkGapOpening <- function(gapOpening, type, substitutionMatrix,

 ##used in MUSCLE, analoguous to checkGapOpening, but only ONE defaut value

 ##function, that tests the input of gapOpening.

-##If the value is negative, everything is ok and the function returns

-##the gapOpening parameter. If the input is positive, the value is transformed

-##and a warning is given. If the input is not numeric, an exception is thrown.

+##If the value is numeric, everything is ok and the function returns

+##the gapOpening parameter. If the input is not numeric, an exception is thrown.

 checkGapOpening2 <- function(gapOpening, substitutionMatrix,

         defaultValue){

     ##set defaultValue

@@ -132,25 +123,18 @@ checkGapOpening2 <- function(gapOpening, substitutionMatrix,

     if (is.numeric(gapOpening)) {

         if (is.matrix(gapOpening)) {

             stop("The parameter gapOpening should be \n",

-                 "a negative numeric, not a matrix!")

+                 "a numeric, not a matrix!")

         }

         if (length(gapOpening) != 1) {

             stop("The parameter gapOpening should be \n",

-                 "a negative numeric, not a vector!")

+                 "a numeric, not a vector!")

         }

         if (is.nan(gapOpening)) {

             stop("The parameter gapOpening should be \n",

-                 "a negative numeric, not a NaN!")

-        }

-        ##check if gapOpening is positive

-        if (gapOpening > 0) {

-            warning("According to BioStrings, the parameter gapOpening \n",

-                    "should be negative! The value is transformed \n",

-                    "to a negative numeric!")

-            gapOpening <- gapOpening * -1;

+                 "a numeric, not a NaN!")

         }

     } else {

-        stop("The parameter gapOpening should be a negative numeric!")

+        stop("The parameter gapOpening should be a numeric!")

     }

     return(gapOpening)

 }

@@ -172,25 +156,18 @@ checkGapExtension <- function(gapExtension, type, substitutionMatrix,

     if (is.numeric(gapExtension)) {

         if (is.matrix(gapExtension)) {

            stop("The parameter gapExtension should be \n",

-                "a negative numeric, not a matrix!")

+                "a numeric, not a matrix!")

         }

         if (length(gapExtension) != 1) {

            stop("The parameter gapExtension should be \n",

-                "a negative numeric, not a vector!")

+                "a numeric, not a vector!")

         }

         if (is.nan(gapExtension)) {

             stop("The parameter gapExtension should be \n",

-                 "a negative numeric, not a NaN!")

-        }

-        ##check if gapExtension is positive

-        if (gapExtension > 0) {

-           warning("According to BioStrings, the parameter gapOpening \n",

-                   "should be negative! The value is transformed to a \n",

-                   "negative numeric.")

-           gapExtension <- gapExtension * -1

+                 "a numeric, not a NaN!")

         }

     } else {

-        stop("The parameter gapExtension should be a negative numeric!")

+        stop("The parameter gapExtension should be a numeric!")

     }

     return(gapExtension)

@@ -6,6 +6,7 @@ msa <- function(inputSeqs,

                 maxiters="default",

                 substitutionMatrix="default",

                 type="default",

+                order=c("aligned", "input"),

                 verbose=FALSE,

                 help=FALSE,

                 ...)

@@ -5,6 +5,7 @@ msaClustalOmega <- function(inputSeqs,

                             maxiters="default",

                             substitutionMatrix="default",

                             type="default",

+                            order=c("aligned", "input"),

                             verbose=FALSE,

                             help=FALSE,

                             ...)

@@ -53,7 +54,15 @@ msaClustalOmega <- function(inputSeqs,

     #############

     # inputSeqs #

     #############

-    inputSeqs <- transformInputSeq(inputSeqs, params[["inputSeqIsFileFlag"]])

+    inputSeqs <- transformInputSeq(inputSeqs)

+

+    #############

+    # order     #

+    #############

+    order <- match.arg(order)

+    params[["outputOrder"]] <- switch(order,

+                                      aligned="tree-order",

+                                      input="input-order")

     ###########

     # cluster #

@@ -103,9 +112,9 @@ msaClustalOmega <- function(inputSeqs,

             substitutionMatrix <- NULL

     } else if (is.character(substitutionMatrix) &&

                    !is.matrix(substitutionMatrix)) {

-            possibleValues <- c("blosum30","blosum40", "blosum50",

-                                "blosum65","blosum80","gonnet")

-            if (!(tolower(substitutionMatrix) %in% possibleValues)){

+            possibleValues <- c("BLOSUM30", "BLOSUM40", "BLOSUM50",

+                                "BLOSUM65", "BLOSUM80", "Gonnet")

+            if (!(substitutionMatrix %in% possibleValues)){

                 ##create a string with all possible Values named text

                 text <- ""

                 text <- paste(possibleValues, collapse=", ")

@@ -117,21 +126,16 @@ msaClustalOmega <- function(inputSeqs,

     ##############

     # gapOpening #

     ##############

-

-    gapOpening <- checkGapOpening(gapOpening, type,

-                                  substitutionMatrix, -6, -6)

-    # ClustalOmega uses positive values

-    gapOpening <- gapOpening * -1

-

+    if (!identical(gapOpening, "default"))

+        warning("msaClustalOmega currently does not support to set\n",

+                "gapOpening to a non-default value!\n")

     ################

     # gapExtension #

     ################

-

-    gapExtension <- checkGapExtension(gapExtension, type,

-                                      substitutionMatrix, -1, -1)

-    # ClustalOmega uses positive values

-    gapExtension <- gapExtension * -1

+    if (!identical(gapExtension, "default"))

+        warning("msaClustalOmega currently does not support to set\n",

+                "gapExtension to a non-default value!\n")

     ############

     # maxiters #

@@ -334,13 +338,13 @@ msaClustalOmega <- function(inputSeqs,

     ##delete param in copy

     paramsCopy[["isProfile"]] <- NULL

-    

+

     #######

     # log #

     #######

     ##Log all non-essential output to this file

     ##DEACTIVATED: All log-messages are print to R console

-    

+

     ##if(!is.null(params[["log"]])) {

     ##    tempList <- checkOutFile("log", params)

     ##    if (tempList$existingFile) {

@@ -349,7 +353,7 @@ msaClustalOmega <- function(inputSeqs,

     ##    }

     ##    params[["log"]] <- tempList$param

     ##}

-    

+

     ##delete param in copy

     ##paramsCopy[["log"]] <- NULL

@@ -468,7 +472,7 @@ msaClustalOmega <- function(inputSeqs,

         if (!identical (params[["outFmt"]], "clustal") &&

             !identical (params[["outFmt"]], "clu")) {

             stop("Until now, the parameter outFmt is only implemented ",

-                 "for value \"clustal\" \n", 

+                 "for value \"clustal\" \n",

                  "the other formats will be ",

                  "realized in a later version.")

         }

@@ -477,23 +481,6 @@ msaClustalOmega <- function(inputSeqs,

     ##delete param in copy

     paramsCopy[["outFmt"]] <- NULL

-    ################

-    # outputOrder #

-    ################

-    ##MSA output orderlike in input/guide-tree

-    ##default: output-order=input-order

-

-    ##possible Values

-    posVal <- c("input-order", "tree-order")

-    ##params[["outputOrder"]] <- checkSingleValParams("outputOrder", params,

-    ##                                                 "input-order", posVal)

-

-    params[["outputOrder"]] <- checkSingleValParamsNew(

-                                "outputOrder", params, posVal)

-

-    ##delete param in copy

-    paramsCopy[["outputOrder"]] <- NULL

-

     #############

     # percentId #

     #############

@@ -523,9 +510,9 @@ msaClustalOmega <- function(inputSeqs,

     if (!is.null(params[["profile2"]])) {

         if (is.null(params[["profile1"]])){

-            stop("The parameter profile1 is NULL, \n", 

+            stop("The parameter profile1 is NULL, \n",

                  "so the parameter profile2 can't have a value! \n",

-                 "Please insert file for parameter profile1 \n", 

+                 "Please insert file for parameter profile1 \n",

                  "or change the parameters profile1 and profile2!")

         }

         checkInFile("profile2", params)

@@ -570,7 +557,7 @@ msaClustalOmega <- function(inputSeqs,

     ##useKimura==TRUE AND percentId==TRUE is not allowed!!!

     if(params[["useKimura"]] & params[["percentId"]]){

-        stop("Percentage Identity cannot be calcuted \n", 

+        stop("Percentage Identity cannot be calcuted \n",

              "if Kimura Distances are used!",

              "You have to set either the parameter percentID or \n",

              "the parameter useKimura to FALSE!")

@@ -622,10 +609,10 @@ msaClustalOmega <- function(inputSeqs,

     inputSeqNames <- names(inputSeqs)

-    names(inputSeqs) <- paste0("seq", 1:length(inputSeqs))

+    names(inputSeqs) <- paste0("Seq", 1:length(inputSeqs))

-    result <- .Call("RClustalOmega", inputSeqs, cluster, gapOpening,

-                    gapExtension, maxiters, substitutionMatrix, type,

+    result <- .Call("RClustalOmega", inputSeqs, cluster, 6,

+                    1, maxiters, substitutionMatrix, type,

                     verbose, params, PACKAGE="msa");

     out <- convertAlnRows(result$msa, type)

@@ -638,7 +625,6 @@ msaClustalOmega <- function(inputSeqs,

     else

         names(out@unmasked) <- NULL

-

     standardParams <- list(gapOpening=gapOpening,

                            gapExtension=gapExtension,

                            maxiters=maxiters,

@@ -5,6 +5,7 @@ msaClustalW <- function(inputSeqs,

                         maxiters="default",

                         substitutionMatrix="default",

                         type="default",

+                        order=c("aligned", "input"),

                         verbose=FALSE,

                         help=FALSE,

                         ...)

@@ -53,7 +54,14 @@ msaClustalW <- function(inputSeqs,

     #############

     # inputSeqs #

     #############

-    inputSeqs <- transformInputSeq(inputSeqs, params[["inputSeqIsFileFlag"]])

+    inputSeqs <- transformInputSeq(inputSeqs)

+

+    #############

+    # order     #

+    #############

+    order <- match.arg(order)

+

+    params[["outorder"]] <- order

     ###########

     # cluster #

@@ -122,7 +130,7 @@ msaClustalW <- function(inputSeqs,

         !is.matrix(substitutionMatrix)) {

         ##check whether value is BLOSUM, PAM, GONNET, or ID;

             possibleValues <- c("blosum", "pam", "gonnet", "id")

-            if (!(tolower(substitutionMatrix) %in% possibleValues)){

+            if (!(substitutionMatrix %in% possibleValues)){

                 ##create a string with all possible Values named text

                 text <- ""

                 text <- paste(possibleValues, collapse=", ")

@@ -135,15 +143,13 @@ msaClustalW <- function(inputSeqs,

         if (isSymmetric(substitutionMatrix)) {

             if (nrow(substitutionMatrix) <=20 ||

                 nrow(substitutionMatrix) >26 ) {

-                    stop("The parameter substitutionMatrix ",

-                         "has wrong dimensions!")

+                    stop("substitutionMatrix has wrong dimensions!")

             }

         } else {

-            stop("The parameter substitutionMatrix should be symmetric!")

+            stop("substitutionMatrix should be a symmetric matrix!")

         }

     }

-

     ##############

     # gapOpening #

     ##############

@@ -351,17 +357,6 @@ msaClustalW <- function(inputSeqs,

     ##delete param in copy

     paramsCopy[["output"]] <- NULL

-    ############

-    # outorder #

-    ############

-

-    ##possible Values

-    posVal <- c("input", "aligned")

-    params[["outorder"]] <- checkSingleValParamsNew("outorder", params, posVal)

-

-    ##delete param in copy

-    paramsCopy[["outorder"]] <- NULL

-

     ########

     # case #

     ########

@@ -617,6 +612,9 @@ msaClustalW <- function(inputSeqs,

     params[["pwgapopen"]] <- checkNumericParamsNew("pwgapopen", params)

+    if (is.numeric(params[["pwgapopen"]]))

+        params[["pwgapopen"]] <- abs(params[["pwgapopen"]])

+

     ##delete param in copy

     paramsCopy[["pwgapopen"]] <- NULL

@@ -627,6 +625,8 @@ msaClustalW <- function(inputSeqs,

     params[["pwgapext"]] <- checkNumericParamsNew("pwgapext", params)

+    if (is.numeric(params[["pwgapext"]]))

+        params[["pwgapext"]] <- abs(params[["pwgapext"]])

     ##delete param in copy

     paramsCopy[["pwgapext"]] <- NULL

@@ -1116,11 +1116,11 @@ msaClustalW <- function(inputSeqs,

     inputSeqNames <- names(inputSeqs)

-    names(inputSeqs) <- paste0("seq", 1:length(inputSeqs))

+    names(inputSeqs) <- paste0("Seq", 1:length(inputSeqs))

-    result <- .Call("RClustalW", inputSeqs, cluster, gapOpening, gapExtension,

-                    maxiters, substitutionMatrix, type, verbose,

-                    params, PACKAGE="msa")

+    result <- .Call("RClustalW", inputSeqs, cluster, abs(gapOpening),

+                    abs(gapExtension), maxiters, substitutionMatrix,

+                    type, verbose, params, PACKAGE="msa")

     out <- convertAlnRows(result$msa, type)

@@ -5,6 +5,7 @@ msaMuscle <- function(inputSeqs,

                       maxiters="default",

                       substitutionMatrix="default",

                       type="default",

+                      order=c("aligned", "input"),

                       verbose=FALSE,

                       help=FALSE,

                       ...)

@@ -70,7 +71,27 @@ msaMuscle <- function(inputSeqs,

     # inputSeqs #

     #############

     ##transform the input Sequences to a string vector

-    inputSeqs <- transformInputSeq(inputSeqs, params[["inputSeqIsFileFlag"]])

+    inputSeqs <- transformInputSeq(inputSeqs)

+

+    #############

+    # order     #

+    #############

+    order <- match.arg(order)

+

+    if (order == "input")

+    {

+        if (params[["inputSeqIsFileFlag"]])

+            stop("msaMuscle does not support order=\"input\" for reading\n",

+                 "sequences directly from a FASTA file.")

+        else if (is.null(names(inputSeqs)) ||

+                 length(unique(names(inputSeqs))) != length(inputSeqs))

+        {

+            warning("order=\"input\" requires input sequences to be named\n",

+                    "uniquely! Assigning default names 'Seq1'..'Seqn'\n",

+                    "to sequences.")

+            names(inputSeqs) <- paste0("Seq", 1:length(inputSeqs))

+        }

+    }

     ###########

     # cluster #

@@ -1126,24 +1147,31 @@ msaMuscle <- function(inputSeqs,

     inputSeqNames <- names(inputSeqs)

-    names(inputSeqs) <- paste0("seq", 1:length(inputSeqs))

-

+    names(inputSeqs) <- paste0("Seq", 1:length(inputSeqs))

-    result <- .Call("RMuscle", inputSeqs, cluster, gapOpening,

-                    gapExtension, maxiters, substitutionMatrix, type,

+    result <- .Call("RMuscle", inputSeqs, cluster, -abs(gapOpening),

+                    -abs(gapExtension), maxiters, substitutionMatrix, type,

                     verbose, params, PACKAGE="msa")

     out <- convertAlnRows(result$msa, type)

     if (length(inputSeqNames) > 0)

     {

-        perm <- match(names(out@unmasked), names(inputSeqs))

-        names(out@unmasked) <- inputSeqNames[perm]

+        if (order == "aligned")

+        {

+            perm <- match(names(out@unmasked), names(inputSeqs))

+            names(out@unmasked) <- inputSeqNames[perm]

+        }

+        else

+        {

+            perm <- match(names(inputSeqs), names(out@unmasked))

+            out@unmasked <- out@unmasked[perm]

+            names(out@unmasked) <- inputSeqNames

+        }

     }

     else

         names(out@unmasked) <- NULL

-

     standardParams <- list(gapOpening=gapOpening,

                            gapExtension=gapExtension,

                            maxiters=maxiters,

@@ -13,7 +13,7 @@ rm -rf src/gc-7.2/*.a

 ## -- Muscle

 rm -rf src/Muscle/muscle.make.std???.txt

 rm -rf src/Muscle/*.o

-rm -rf src/Muscle/*.dll

+rm -rf src/Muscle/*.a

 rm -rf src/Muscle/*.dll

 ## -- ClustalW

@@ -1,5 +1,5 @@

 Change history of package msa:

 ==============================

-Version 0.99.0:

-- first version submitted to Bioconductor

+Version 1.0.0:

+- first official release as part of Bioconductor 3.1

@@ -1,68 +1,68 @@

->HBA1 Homo sapiens

+>HBA1_Homo_sapiens

 VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGK

 KVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPA

 VHASLDKFLASVSTVLTSKYR

->HBA1 Macaca mulatta

+>HBA1_Macaca_mulatta

 VLSPADKSNVKAAWGKVGGHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGK

 KVADALTLAVGHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPA

 VHASLDKFLASVSTVLTSKYR

->HBA1 Ornithorhynchus anatinus

+>HBA1_Ornithorhynchus_anatinus

 MLTDAEKKEVTALWGKAAGHGEEYGAEALERLFQAFPTTKTYFSHFDLSHGSAQIKAHGK

 KVADALSTAAGHFDDMDSALSALSDLHAHKLRVDPVNFKLLAHCILVVLARHCPGEFTPS

 AHAAMDKFLSKVATVLTSKYR

->HBA1 Bos taurus

+>HBA1_Bos_taurus

 VLSAADKGNVKAAWGKVGGHAAEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGA

 KVAAALTKAVEHLDDLPGALSELSDLHAHKLRVDPVNFKLLSHSLLVTLASHLPSDFTPA

 VHASLDKFLANVSTVLTSKYR

->HBA1 Monodelphis domestica

+>HBA1_Monodelphis_domestica

 VLSAADKTNVKAAWSKVGGNSGAYMGEALYRTFLSFPPTKTYFPHFEFSAGSAQIKGQGQ

 KIADAVSLAVAHMDDLATALSALSDLHAHNLKVDPVNFKFLCHNVLVTLASHLGKDFTPE

 IHASLDKFLALLSTVLTSKYR

->HBA1 Erinaceus europaeus

+>HBA1_Erinaceus_europaeus

 VLSATDKANVKTFWGKLGGHGGEYGGEALDRMFQAHPTTKTYFPHFDLNPGSAQVKGHGK

 KVADALTTAVNNLDDVPGALSALSDLHAHKLRVDPVNFKLLSHCLLVTLALHHPADFTPA

 VHASLDKFLATVATVLTSKYR

->HBA1 Loxodonta africana

+>HBA1_Loxodonta_africana

 VLSDNDKTNVKATWSKVGDHASDYVAEALERMFFSFPTTKTYFPHFDLGHGSGQVKAHGK

 KVGEALTQAVGHLDDLPSALSALSDLHAHKLRVDPVNFKLLSHCLLVTLSSHQPTEFTPE

 VHASLDKFLSNVSTVLTSKYR

->HBA1 Mus musculus

+>HBA1_Mus_musculus

 VLSGEDKSNIKAAWGKIGGHGAEYGAEALERMFASFPTTKTYFPHFDVSHGSAQVKGHGK

 KVADALASAAGHLDDLPGALSALSDLHAHKLRVDPVNFKLLSHCLLVTLASHHPADFTPA

 VHASLDKFLASVSTVLTSKYR

->HBA1 Felis silvestris catus

+>HBA1_Felis_silvestris_catus

 VLSAADKSNVKACWGKIGSHAGEYGAEALERTFCSFPTTKTYFPHFDLSHGSAQVKAHGQ

 KVADALTQAVAHMDDLPTAMSALSDLHAYKLRVDPVNFKFLSHCLLVTLACHHPAEFTPA

 VHASLDKFFSAVSTVLTSKYR

->HBA1 Chrysocyon brachyurus

+>HBA1_Chrysocyon_brachyurus

 VLSPADKTNIKSTWDKIGGHAGDYGGEALDRTFQSFPTTKTYFPHFDLSPGSAQVKAHGK

 KVADALTTAVAHLDDLPGALSALSDLHAYKLRVDPVNFKLLSHCLLVTLACHHPTEFTPA

 VHASLDKFFTAVSTVLTSKYR

->HBA1 Gallus gallus

+>HBA1_Gallus_gallus

 VLSAADKNNVKGIFTKIAGHAEEYGAETLERMFTTYPPTKTYFPHFDLSHGSAQIKGHGK

 KVVAALIEAANHIDDIAGTLSKLSDLHAHKLRVDPVNFKLLGQCFLVVVAIHHPAALTPE

 VHASLDKFLCAVGTVLTAKYR

->Zebra_fish (Brachydanio rerio)x

+>HBA1_Danio_rerio

 SLSDTDKAVVKAIWAKISPKADEIGAEALARMLTVYPQTKTYFSHWADLSPGSGPVKKHG

 KTIMGAVGEAISKIDDLVGGLAALSELHAFKLRVDPANFKILSHNVIVVIAMLFPADFTP

 EVHVSVDKFFNNLALALSEKYR

->HBA1 Tursiops truncatus

+>HBA1_Tursiops_truncatus

 VLSPADKTNVKGTWSKIGNHSAEYGAEALERMFINFPSTKTYFSHFDLGHGSAQIKGHGK

 KVADALTKAVGHIDNLPDALSELSDLHAHKLRVDPVNFKLLSHCLLVTLALHLPADFTPS

 VHASLDKFLASVSTVLTSKYR

->HBA1 Xenopus tropicalis

+>HBA1_Xenopus_tropicalis

 HLTADDKKHIKAIWPSVAAHGDKYGGEALHRMFMCAPKTKTYFPDFDFSEHSKHILAHGK

 KVSDALNEACNHLDNIAGCLSKLSDLHAYDLRVDPGNFPLLAHQILVVVAIHFPKQFDPA

 THKALDKFLVSVSNVLTSKYR

->HBA1 Microcephalophis gracilis

+>HBA1_Microcephalophis_gracilis

 VLTEEDKARVRVAWVPVSKNAELYGAETLTRLFAAHPTTKTYFPHFDLSPGSNDLKVHGK

 KVIDALTEAVNNLDDVAGALSKLSDLHAQKLRVDPDNFQFLGLCLEVTIAAHSGGPLKPE

 VLLSVDKFLGQISKVLASRYR

->HBA1 Pan troglodytes

+>HBA1_Pan_troglodytes

 MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHG

 KKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTP

 AVHASLDKFLASVSTVLTSKYR

->HBA1 Rattus norvegicus

+>HBA1_Rattus_norvegicus

 MVLSADDKTNIKNCWGKIGGHGGEYGEEALQRMFAAFPTTKTYFSHIDVSPGSAQVKAHG

 KKVADALAKAADHVEDLPGALSTLSDLHAHKLRVDPVNFKFLSHCLLVTLACHHPGDFTP

 AMHASLDKFLASVSTVLTSKYR

@@ -1,4 +1,4 @@

->PH4H Homo sapiens

+>PH4H_Homo_sapiens

 MSTAVLENPGLGRKLSDFGQETSYIEDNCNQNGAISLIFSLKEEVGALAKVLRLFEENDV

 NLTHIESRPSRLKKDEYEFFTHLDKRSLPALTNIIKILRHDIGATVHELSRDKKKDTVPW

 FPRTIQELDRFANQILSYGAELDADHPGFKDPVYRARRKQFADIAYNYRHGQPIPRVEYM

@@ -7,7 +7,7 @@ RLRPVAGLLSSRDFLGGLAFRVFHCTQYIRHGSKPMYTPEPDICHELLGHVPLFSDRSFA

 QFSQEIGLASLGAPDEYIEKLATIYWFTVEFGLCKQGDSIKAYGAGLLSSFGELQYCLSE

 KPKLLPLELEKTAIQNYTVTEFQPLYYVAESFNDAKEKVRNFAATIPRPFSVRYDPYTQR

 IEVLDNTQQLKILADSINSEIGILCSALQKIK

->PH4H Rattus norvegicus

+>PH4H_Rattus_norvegicus

 MAAVVLENGVLSRKLSDFGQETSYIEDNSNQNGAISLIFSLKEEVGALAKVLRLFEENDI

 NLTHIESRPSRLNKDEYEFFTYLDKRTKPVLGSIIKSLRNDIGATVHELSRDKEKNTVPW

 FPRTIQELDRFANQILSYGAELDADHPGFKDPVYRARRKQFADIAYNYRHGQPIPRVEYT

@@ -16,7 +16,7 @@ RLRPVAGLLSSRDFLGGLAFRVFHCTQYIRHGSKPMYTPEPDICHELLGHVPLFSDRSFA

 QFSQEIGLASLGAPDEYIEKLATIYWFTVEFGLCKEGDSIKAYGAGLLSSFGELQYCLSD

 KPKLLPLELEKTACQEYSVTEFQPLYYVAESFSDAKEKVRTFAATIPRPFSVRYDPYTQR

 VEVLDNTQQLKILADSINSEVGILCNALQKIKS

->PH4H Mus musculus

+>PH4H_Mus_musculus

 MAAVVLENGVLSRKLSDFGQETSYIEDNSNQNGAVSLIFSLKEEVGALAKVLRLFEENEI

 NLTHIESRPSRLNKDEYEFFTYLDKRSKPVLGSIIKSLRNDIGATVHELSRDKEKNTVPW

 FPRTIQELDRFANQILSYGAELDADHPGFKDPVYRARRKQFADIAYNYRHGQPIPRVEYT

@@ -25,19 +25,19 @@ RLRPVAGLLSSRDFLGGLAFRVFHCTQYIRHGSKPMYTPEPDICHELLGHVPLFSDRSFA

 QFSQEIGLASLGAPDEYIEKLATIYWFTVEFGLCKEGDSIKAYGAGLLSSFGELQYCLSD

 KPKLLPLELEKTACQEYTVTEFQPLYYVAESFNDAKEKVRTFAATIPRPFSVRYDPYTQR

 VEVLDNTQQLKILADSINSEVGILCHALQKIKS

->PH4H Chromobacterium violaceum

+>PH4H_Chromobacterium_violaceum

 MNDRADFVVPDITTRKNVGLSHDANDFTLPQPLDRYSAEDHATWATLYQRQCKLLPGRAC

 DEFMEGLERLEVDADRVPDFNKLNQKLMAATGWKIVAVPGLIPDDVFFEHLANRRFPVTW

 WLREPHQLDYLQEPDVFHDLFGHVPLLINPVFADYLEAYGKGGVKAKALGALPMLARLYW

 YTVEFGLINTPAGMRIYGAGILSSKSESIYCLDSASPNRVGFDLMRIMNTRYRIDTFQKT

 YFVIDSFKQLFDATAPDFAPLYLQLADAQPWGAGDVAPDDLVLNAGDRQGWADTEDV

->PH4H Pseudomonas aeruginosa

+>PH4H_Pseudomonas_aeruginosa

 MKTTQYVARQPDDNGFIHYPETEHQVWNTLITRQLKVIEGRACQEYLDGIEQLGLPHERI

 PQLDEINRVLQATTGWRVARVPALIPFQTFFELLASQQFPVATFIRTPEELDYLQEPDIF

 HEIFGHCPLLTNPWFAEFTHTYGKLGLKASKEERVFLARLYWMTIEFGLVETDQGKRIYG

 GGILSSPKETVYSLSDEPLHQAFNPLEAMRTPYRIDILQPLYFVLPDLKRLFQLAQEDIM

 ALVHEAMRLGLHAPLFPPKQAA

->PH4H Bos taurus

+>PH4H_Bos_taurus

 MSALVLESRALGRKLSDFGQETSYIEGNSDQNAVSLIFSLKEEVGALARVLRLFEENDIN

 LTHIESRPSRLRKDEYEFFTNLDQRSVPALANIIKILRHDIGATVHELSRDKKKDTVPWF

 PRTIQELDNFANQVLSYGAELDADHPGFKDPVYRARRKQFADIAYNYRHGQPIPRVEYTE

@@ -46,20 +46,20 @@ LRPVAGLLSSRDFLGGLAFRVFHCTQYIRHGSKPMYTPEPDICHELLGHVPLFSDRSFAQ

 FSQEIGLASLGAPDEYIEKLATIYWFTVEFGLCKQGDSIKAYGAGLLSSFGELQYCLSDK

 PKLLPLELEKTAVQEYTITEFQPLYYVAESFNDAKEKVRNFAATIPRPFSVHYDPYTQRI

 EVLDNTQQLKILADSISSEVEILCSALQKLK

->PH4H Ralstonia solanacearum

+>PH4H_Ralstonia_solanacearum

 MAIATPTSAAPTPAPAGFTGTLTDKLREQFAEGLDGQTLRPDFTMEQPVHRYTAADHATW

 RTLYDRQEALLPGRACDEFLQGLSTLGMSREGVPSFDRLNETLMRATGWQIVAVPGLVPD

 EVFFEHLANRRFPASWWMRRPDQLDYLQEPDGFHDIFGHVPLLINPVFADYMQAYGQGGL

 KAARLGALDMLARLYWYTVEFGLIRTPAGLRIYGAGIVSSKSESVYALDSASPNRIGFDV

 HRIMRTRYRIDTFQKTYFVIDSFEQLFDATRPDFTPLYEALGTLPTFGAGDVVDGDAVLN

 AGTREGWADTADI

->PH4H Caulobacter crescentus

+>PH4H_Caulobacter_crescentus

 MSGDGLSNGPPPGARPDWTIDQGWETYTQAEHDVWITLYERQTDMLHGRACDEFMRGLDA

 LDLHRSGIPDFARINEELKRLTGWTVVAVPGLVPDDVFFDHLANRRFPAGQFIRKPHELD

 YLQEPDIFHDVFGHVPMLTDPVFADYMQAYGEGGRRALGLGRLANLARLYWYTVEFGLMN

 TPAGLRIYGAGIVSSRTESIFALDDPSPNRIGFDLERVMRTLYRIDDFQQVYFVIDSIQT

 LQEVTLRDFGAIYERLASVSDIGVAEIVPGDAVLTRGTQAYATAGGRLAGAAAG

->PH4H Rhizobium loti

+>PH4H_Rhizobium_loti

 MSVAEYARDCAAQGLRGDYSVCRADFTVAQDYDYSDEEQAVWRTLCDRQTKLTRKLAHHS

 YLDGVEKLGLLDRIPDFEDVSTKLRKLTGWEIIAVPGLIPAAPFFDHLANRRFPVTNWLR

 TRQELDYIVEPDMFHDFFGHVPVLSQPVFADFMQMYGKKAGDIIALGGDEMITRLYWYTA

@@ -1,4 +1,4 @@

->PAH Homo sapiens

+>PAH_Homo_sapiens

 CAGCTGGGGGTAAGGGGGGCGGATTATTCATATAATTGTTATACCAGACGGTCGCAGGCTTAGTCCAATT

 GCAGAGAACTCGCTTCCCAGGCTTCTGAGAGTCCCGGAAGTGCCTAAACCTGTCTAATCGACGGGGCTTG

 GGTGGCCCGTCGCTCCCTGGCTTCTTCCCTTTACCCAGGGCGGGCAGCGAAGTGGTGCCTCCTGCGTCCC

@@ -38,7 +38,7 @@ ACTCTGCACCTAATCCCCATAACTTCCAGTATCATTTTCCAATTAATTATCAAGTCTGTTTTGGGAAACA

 CTTTGAGGACATTTATGATGCAGCAGATGTTGACTAAAGGCTTGGTTGGTAGATATTCAGGAAATGTTCA

 CTGAATAAATAAGTAAATACATTATTGAAAAGCAAATCTGTATAAATGTGAAATTTTTATTTGTATTAGT

 AATAAAACATTAGTAGTTTA

->PAH Mus musculus

+>PAH_Mus_musculus

 AGTCCAGGACTGGAGTTGGGTATGGACTGTTCATGTCTATCCACTGCTACGTCAGGGCAACACCCACTGA

 GAGTGACCTTGTAGACTGCAGTGGGAGACACCCTTCAAAACCTCTCCTCTCCTGTCCTGAGAGCCAGGTT

 AAAACCATCAGCCCCGCATCCTGAGTGCAAACTTTTCCTAACCCTGCTGCTAAGCTAGACACCTCACTTA

@@ -70,7 +70,7 @@ CATTTGGGCTCTGTCTGTTCATTTTTAACCTCTCAGGTAAGCTCTGATGGAATACATATTGCTTAGTGTA

 AAATGTGAGACTGTCATCGGGAACAAATTATTCCATTCAGTACAGATTGTAATCTACAAAGCTTAGTTTC

 TACATTCATTCATTATGGCTCTGAGAACTACTTTGTTAGCCTGCTTACATAAATGTCCTCTGATCTAAGA

 CTCTATTAAGATAGTTACAAGCAATAAAGCATTATATAAAACAAAAAAAAAA

->PAH Rattus norvegicus

+>PAH_Rattus_norvegicus

 CAAGTTAAAACCATCAGCCCTCCCATCCTGAGTGCCTACCTTTCCCAACCCCGCTGCTAAGCTAGACACC

 TCACTCACTGAGAGCCAGCATGGCAGCTGTTGTCCTGGAGAATGGAGTCCTGAGCAGAAAACTCTCAGAC

 TTTGGGCAGGAAACAAGCTATATTGAAGACAACTCCAATCAAAATGGTGCCATATCTCTGATATTCTCAC

@@ -1,4 +1,4 @@

->PAH Homo sapiens

+>PAH_Homo_sapiens

 CAGCUGGGGGUAAGGGGGGCGGAUUAUUCAUAUAAUUGUUAUACCAGACGGUCGCAGGCUUAGUCCAAUU

 GCAGAGAACUCGCUUCCCAGGCUUCUGAGAGUCCCGGAAGUGCCUAAACCUGUCUAAUCGACGGGGCUUG

 GGUGGCCCGUCGCUCCCUGGCUUCUUCCCUUUACCCAGGGCGGGCAGCGAAGUGGUGCCUCCUGCGUCCC

@@ -38,7 +38,7 @@ ACUCUGCACCUAAUCCCCAUAACUUCCAGUAUCAUUUUCCAAUUAAUUAUCAAGUCUGUUUUGGGAAACA

 CUUUGAGGACAUUUAUGAUGCAGCAGAUGUUGACUAAAGGCUUGGUUGGUAGAUAUUCAGGAAAUGUUCA

 CUGAAUAAAUAAGUAAAUACAUUAUUGAAAAGCAAAUCUGUAUAAAUGUGAAAUUUUUAUUUGUAUUAGU

 AAUAAAACAUUAGUAGUUUA

->PAH Mus musculus

+>PAH_Mus_musculus

 AGUCCAGGACUGGAGUUGGGUAUGGACUGUUCAUGUCUAUCCACUGCUACGUCAGGGCAACACCCACUGA

 GAGUGACCUUGUAGACUGCAGUGGGAGACACCCUUCAAAACCUCUCCUCUCCUGUCCUGAGAGCCAGGUU

 AAAACCAUCAGCCCCGCAUCCUGAGUGCAAACUUUUCCUAACCCUGCUGCUAAGCUAGACACCUCACUUA

@@ -70,7 +70,7 @@ CAUUUGGGCUCUGUCUGUUCAUUUUUAACCUCUCAGGUAAGCUCUGAUGGAAUACAUAUUGCUUAGUGUA

 AAAUGUGAGACUGUCAUCGGGAACAAAUUAUUCCAUUCAGUACAGAUUGUAAUCUACAAAGCUUAGUUUC

 UACAUUCAUUCAUUAUGGCUCUGAGAACUACUUUGUUAGCCUGCUUACAUAAAUGUCCUCUGAUCUAAGA

 CUCUAUUAAGAUAGUUACAAGCAAUAAAGCAUUAUAUAAAACAAAAAAAAAA

->PAH Rattus norvegicus

+>PAH_Rattus_norvegicus

 CAAGUUAAAACCAUCAGCCCUCCCAUCCUGAGUGCCUACCUUUCCCAACCCCGCUGCUAAGCUAGACACC

 UCACUCACUGAGAGCCAGCAUGGCAGCUGUUGUCCUGGAGAAUGGAGUCCUGAGCAGAAAACUCUCAGAC

 UUUGGGCAGGAAACAAGCUAUAUUGAAGACAACUCCAAUCAAAAUGGUGCCAUAUCUCUGAUAUUCUCAC

@@ -12,8 +12,8 @@ distMatOut=                  [Filename]

 force=                       [Logical Value]

 full=                        [Logical Value]

 fullIter=                    [Logical Value]

-gapOpening=                  [Negative Numeric]

-gapExtension=                [Negative Numeric]

+gapOpening=                  [Numeric] (currently not supported)

+gapExtension=                [Numeric] (currently not supported)

 guideTreeIn=                 [Filename]

 guideTreeOut=                [Filename]

 help=                        [Logical Value]

@@ -28,9 +28,9 @@ maxHmmIterations=            [Int]

 maxiters=                    [Positive Int]

 maxNumSeq=                   [Int]

 maxSeqLen=                   [Int]

+order=                       [String]

 outfile=                     [Filename]

 outFmt=                      [String]

-outputOrder=                 [String]

 percentId=                   [Logical Value]

 profile1=                    [Filename]

 profile2=                    [Filename]

@@ -13,8 +13,8 @@ dnamatrix=                   [Filename] or [String]

 endgaps=                     [Logical Value]

 fullhelp=                    [Logical Value]

 gapdist=                     [Int]

-gapOpening=                  [Negative Numeric]

-gapExtension=                [Negative Numeric]

+gapOpening=                  [Numeric]

+gapExtension=                [Numeric]

 helixendin=                  [Int]

 helixendout=                 [Int]

 helixgap=                    [Int]

@@ -34,7 +34,7 @@ nosecstr2=                   [Logical Value]

 novgap=                      [Logical Value]

 noweights=                   [Logical Value]

 options=                     [Logical Value]

-outorder=                    [String]

+order=                       [String]

 output=                      [String]

 outputtree=                  [String]

 pairgap=                     [Int]

@@ -20,8 +20,8 @@ diags2=                      [Logical Value]

 dimer=                       [Logical Value]

 distance1=                   [String]

 distance2=                   [String]

-gapOpening=                  [Negative Numeric]

-gapExtension=                [Negative Numeric]

+gapOpening=                  [Numeric]

+gapExtension=                [Numeric]

 hydro=                       [Positive Int]

 hydrofactor=                 [Positive Numeric]

 in1=                         [Filename]

@@ -36,6 +36,7 @@ minsmoothscore=              [Positive Numeric]

 noanchors=                   [Logical Value]

 nocore=                      [Logical Value]

 objscore=                    [String]

+order=                       [String]

 profile=                     [Logical Value]

 refine=                      [Logical Value]

 refinew=                     [Logical Value]

@@ -11,7 +11,8 @@

         cluster="default", gapOpening="default",

         gapExtension="default", maxiters="default",

         substitutionMatrix="default", type="default",

-        verbose=FALSE, help=FALSE, ...)

+        order=c("aligned", "input"), verbose=FALSE, help=FALSE,

+        ...)

 }

 \arguments{

   \item{inputSeqs}{input sequences; this argument can be a character vector,

@@ -31,16 +32,16 @@

     \code{\link{msaMuscle}} for algorithm-specific information.}

   \item{gapOpening}{gap opening penalty; the defaults are

     specific to the algorithm (see \code{\link{msaClustalW}},

-    \code{\link{msaClustalOmega}}, or \code{\link{msaMuscle}});

-    In order to standardize interfaces,

-    all algorithms consistently use negative values for the gap opening

-    penalty.}

+    and \code{\link{msaMuscle}}). Note that the sign of

+    this parameter is ignored. The sign is automatically

+    adjusted such that the called algorithm penalizes gaps

+    instead of rewarding them.}

   \item{gapExtension}{gap extension penalty; the defaults are

     specific to the algorithm (see \code{\link{msaClustalW}},

-    \code{\link{msaClustalOmega}}, or \code{\link{msaMuscle}});

-    In order to standardize interfaces,

-    all algorithms consistently use negative values for the gap extension

-    penalty.}

+    and \code{\link{msaMuscle}}). Note that the sign of

+    this parameter is ignored. The sign is automatically

+    adjusted such that the called algorithm penalizes gaps