msaConvert: Convert Multiple Sequence Alignment for Other Packages

Description Usage Arguments Details Value Author(s) References See Also Examples

View source: R/msaConvert.R

Description

This function converts a multiple sequence alignment object to formats used in other sequence analysis packages.

Usage

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    msaConvert(x,
               type=c("seqinr::alignment", "bios2mds::align",
                      "ape::AAbin", "ape::DNAbin",
                      "phangorn::phyDat", "bio3d::fasta"))

Arguments

x

an object of class MultipleAlignment (which includes objects of classes MsaAAMultipleAlignment, MsaDNAMultipleAlignment, and MsaRNAMultipleAlignment)

type

a character string specifying to which type of object x should be converted; currently, the values "seqinr::alignment", "bios2mds::align", "ape::AAbin", "ape::DNAbin", "phangorn::phyDat", and "bio3d::fasta".

Details

The function converts x to the class of object as specified by the type argument. The values possible for the type argument follow the same principle pkg::cl, i.e. x is converted to class cl as defined in the pkg package.

The conversions for usage by the packages seqinr, bios2mds, and ape work independently of these packages and do not strictly require these packages. They need not even be installed. This approach has been chosen to avoid abundant dependencies and possible incompatibilities. That is also why the standard S3/S4 mechanism of as/as.class functions is not used.

The conversion to the phyDat class can be done easily using the as.phyDat function from the phangorn package. The msaConvert function still provides this conversion for the sake of consistency. However, this conversion is just a wrapper function around the as.phyDat function from the phangorn package. Thus, the phangorn package needs to be installed.

The conversion "ape::AAbin" only works for multiple alignments of amino acid sequences, while the conversions "ape::DNAbin" and "phangorn::phyDat" only work for multiple alignments of DNA sequences. When converting to "ape::AAbin", gaps/dashes are replaced by ‘X’. Moreover, conversions to "ape::DNAbin" also convert all characters to lowercase and replace gaps/dashes by ‘n’.

Value

The function returns an object of the class as specified by the type argument.

Author(s)

Ulrich Bodenhofer <[email protected]>

References

http://www.bioinf.jku.at/software/msa

U. Bodenhofer, E. Bonatesta, C. Horejs-Kainrath, and S. Hochreiter (2015). msa: an R package for multiple sequence alignment. Bioinformatics 31(24):3997-3999. DOI: 10.1093/bioinformatics/btv494.

See Also

msa, MsaAAMultipleAlignment, MsaDNAMultipleAlignment, MsaRNAMultipleAlignment, MsaMetaData

Examples

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## read sequences
filepath <- system.file("examples", "exampleAA.fasta", package="msa")
mySeqs <- readAAStringSet(filepath)

## perform multiple alignment
myAlignment <- msa(mySeqs)

## convert to an object of class 'alignment' (package 'seqinr')
msaConvert(myAlignment, "seqinr::alignment")

## convert to an object of class 'align' (package 'bios2mds')
msaConvert(myAlignment, "bios2mds::align")

Example output

Loading required package: Biostrings
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

use default substitution matrix
$nb
[1] 9

$nam
[1] "PH4H_Rattus_norvegicus"         "PH4H_Mus_musculus"             
[3] "PH4H_Homo_sapiens"              "PH4H_Bos_taurus"               
[5] "PH4H_Chromobacterium_violaceum" "PH4H_Ralstonia_solanacearum"   
[7] "PH4H_Caulobacter_crescentus"    "PH4H_Pseudomonas_aeruginosa"   
[9] "PH4H_Rhizobium_loti"           

$seq
[1] "MAAVVLENGVLSRKLSDFGQETSYIEDNSNQNGAISLIFSLKEEVGALAKVLRLFEENDINLTHIESRPSRLNKDEYEFFTYLDKRTKPVLGSIIKSLRNDIGATVHELSRDKEKNTVPWFPRTIQELDRFANQILSYGAELDADHPGFKDPVYRARRKQFADIAYNYRHGQPIPRVEYTEEEKQTWGTVFRTLKALYKTHACYEHNHIFPLLEKYCGFREDNIPQLEDVSQFLQTCTGFRLRPVAGLLSSRDFLGGLAFRVFHCTQYIRHGSKPMYTPEPDICHELLGHVPLFSDRSFAQFSQEIG-LASLGAPDEYIEKLATIYWFTVEFGLCKEG-DSIKAYGAGLLSSFGELQYCLSD-KPKLLPLELEKTACQEYSVTEFQPLYYVAESFSDAKEKVRTFAATIPRPFSVRYDPYTQRVEVLDNTQQLKILADSINSEVGILCNALQKIKS"
[2] "MAAVVLENGVLSRKLSDFGQETSYIEDNSNQNGAVSLIFSLKEEVGALAKVLRLFEENEINLTHIESRPSRLNKDEYEFFTYLDKRSKPVLGSIIKSLRNDIGATVHELSRDKEKNTVPWFPRTIQELDRFANQILSYGAELDADHPGFKDPVYRARRKQFADIAYNYRHGQPIPRVEYTEEERKTWGTVFRTLKALYKTHACYEHNHIFPLLEKYCGFREDNIPQLEDVSQFLQTCTGFRLRPVAGLLSSRDFLGGLAFRVFHCTQYIRHGSKPMYTPEPDICHELLGHVPLFSDRSFAQFSQEIG-LASLGAPDEYIEKLATIYWFTVEFGLCKEG-DSIKAYGAGLLSSFGELQYCLSD-KPKLLPLELEKTACQEYTVTEFQPLYYVAESFNDAKEKVRTFAATIPRPFSVRYDPYTQRVEVLDNTQQLKILADSINSEVGILCHALQKIKS"
[3] "MSTAVLENPGLGRKLSDFGQETSYIEDNCNQNGAISLIFSLKEEVGALAKVLRLFEENDVNLTHIESRPSRLKKDEYEFFTHLDKRSLPALTNIIKILRHDIGATVHELSRDKKKDTVPWFPRTIQELDRFANQILSYGAELDADHPGFKDPVYRARRKQFADIAYNYRHGQPIPRVEYMEEEKKTWGTVFKTLKSLYKTHACYEYNHIFPLLEKYCGFHEDNIPQLEDVSQFLQTCTGFRLRPVAGLLSSRDFLGGLAFRVFHCTQYIRHGSKPMYTPEPDICHELLGHVPLFSDRSFAQFSQEIG-LASLGAPDEYIEKLATIYWFTVEFGLCKQG-DSIKAYGAGLLSSFGELQYCLSE-KPKLLPLELEKTAIQNYTVTEFQPLYYVAESFNDAKEKVRNFAATIPRPFSVRYDPYTQRIEVLDNTQQLKILADSINSEIGILCSALQKIK-"
[4] "MSALVLESRALGRKLSDFGQETSYIEGNSDQN-AVSLIFSLKEEVGALARVLRLFEENDINLTHIESRPSRLRKDEYEFFTNLDQRSVPALANIIKILRHDIGATVHELSRDKKKDTVPWFPRTIQELDNFANQVLSYGAELDADHPGFKDPVYRARRKQFADIAYNYRHGQPIPRVEYTEEEKKTWGTVFRTLKSLYKTHACYEHNHIFPLLEKYCGFREDNIPQLEEVSQFLQSCTGFRLRPVAGLLSSRDFLGGLAFRVFHCTQYIRHGSKPMYTPEPDICHELLGHVPLFSDRSFAQFSQEIG-LASLGAPDEYIEKLATIYWFTVEFGLCKQG-DSIKAYGAGLLSSFGELQYCLSD-KPKLLPLELEKTAVQEYTITEFQPLYYVAESFNDAKEKVRNFAATIPRPFSVHYDPYTQRIEVLDNTQQLKILADSISSEVEILCSALQKLK-"
[5] "------------------------------------------------------------------------------------------------------------------------------------MNDRADFVVPD-----ITTRKNVGLSHDAN------DFTLPQPLDRYSAEDHATWATLYQRQCKLLPGRACDEFMEGL----ERLEVDADRVPDFNKLNQKLMAATGWKIVAVPGLIPDDVFFEHLANRRFPVTWWLREPHQLDYLQEPDVFHDLFGHVPLLINPVFADYLEAYGKGGVKAKALGALPMLARLYWYTVEFGLINTP-AGMRIYGAGILSSKSESIYCLDSASPNRVGFDLMRIMNTRYRIDTFQKTYFVIDSFKQLFDATA-PDFAPLYLQLADAQPWGAGDVAPDDLVLNAGDRQGWADTEDV----------"
[6] "-------------------------------------------------------------------------------------------------------------------------------MAIATPTSAAPTPAPAGFTGTLTDKLREQFAEGLDGQTLRPDFTMEQPVHRYTAADHATWRTLYDRQEALLPGRACDEFLQGL----STLGMSREGVPSFDRLNETLMRATGWQIVAVPGLVPDEVFFEHLANRRFPASWWMRRPDQLDYLQEPDGFHDIFGHVPLLINPVFADYMQAYGQGGLKAARLGALDMLARLYWYTVEFGLIRTP-AGLRIYGAGIVSSKSESVYALDSASPNRIGFDVHRIMRTRYRIDTFQKTYFVIDSFEQLFDATR-PDFTPLYEALGTLPTFGAGDVVDGDAVLNAGTREGWADTADI----------"
[7] "------------------------------------------------------------------------------------------------------------------------------------MSG---------------DGLSNGPPPGAR-----PDWTIDQGWETYTQAEHDVWITLYERQTDMLHGRACDEFMRGL----DALDLHRSGIPDFARINEELKRLTGWTVVAVPGLVPDDVFFDHLANRRFPAGQFIRKPHELDYLQEPDIFHDVFGHVPMLTDPVFADYMQAYGEGGRRALGLGRLANLARLYWYTVEFGLMNTP-AGLRIYGAGIVSSRTESIFALDDPSPNRIGFDLERVMRTLYRIDDFQQVYFVIDSIQTLQEVTL-RDFGAIYERLASVSDIGVAEIVPGDAVLTRGT-QAYATAGGRLAGAAAG---"
[8] "------------------------------------------------------------------------------------------------------------------------------------------------------MKTTQYVARQPD----------DNGFIHYPETEHQVWNTLITRQLKVIEGRACQEYLDGI----EQLGLPHERIPQLDEINRVLQATTGWRVARVPALIPFQTFFELLASQQFPVATFIRTPEELDYLQEPDIFHEIFGHCPLLTNPWFAEFTHTYGKLGLKASKE-ERVFLARLYWMTIEFGLVETD-QGKRIYGGGILSSPKETVYSLSD-EPLHQAFNPLEAMRTPYRIDILQPLYFVLPDLKRLFQLAQ-EDIMALVHEAMRLG-LHAPLFPPKQAA-------------------------"
[9] "------------------------------------------------------------------------------------------------------------------------------------MSVAEYAR----------DCAAQGLRGDYS--VCRADFTVAQDYD-YSDEEQAVWRTLCDRQTKLTRKLAHHSYLDGV----EKLGL-LDRIPDFEDVSTKLRKLTGWEIIAVPGLIPAAPFFDHLANRRFPVTNWLRTRQELDYIVEPDMFHDFFGHVPVLSQPVFADFMQMYGKKAGDIIALGGDEMITRLYWYTAEYGLVQEAGQPLKAFGAGLMSSFTELQFAVEGKDAHHVPFDLETVMRTGYEIDKFQRAYFVLPSFDALRDAFQTADFEAIVARRKDQKALDPATV-------------------------------"

$com
[1] NA

attr(,"class")
[1] "alignment"
$PH4H_Rattus_norvegicus
  [1] "M" "A" "A" "V" "V" "L" "E" "N" "G" "V" "L" "S" "R" "K" "L" "S" "D" "F"
 [19] "G" "Q" "E" "T" "S" "Y" "I" "E" "D" "N" "S" "N" "Q" "N" "G" "A" "I" "S"
 [37] "L" "I" "F" "S" "L" "K" "E" "E" "V" "G" "A" "L" "A" "K" "V" "L" "R" "L"
 [55] "F" "E" "E" "N" "D" "I" "N" "L" "T" "H" "I" "E" "S" "R" "P" "S" "R" "L"
 [73] "N" "K" "D" "E" "Y" "E" "F" "F" "T" "Y" "L" "D" "K" "R" "T" "K" "P" "V"
 [91] "L" "G" "S" "I" "I" "K" "S" "L" "R" "N" "D" "I" "G" "A" "T" "V" "H" "E"
[109] "L" "S" "R" "D" "K" "E" "K" "N" "T" "V" "P" "W" "F" "P" "R" "T" "I" "Q"
[127] "E" "L" "D" "R" "F" "A" "N" "Q" "I" "L" "S" "Y" "G" "A" "E" "L" "D" "A"
[145] "D" "H" "P" "G" "F" "K" "D" "P" "V" "Y" "R" "A" "R" "R" "K" "Q" "F" "A"
[163] "D" "I" "A" "Y" "N" "Y" "R" "H" "G" "Q" "P" "I" "P" "R" "V" "E" "Y" "T"
[181] "E" "E" "E" "K" "Q" "T" "W" "G" "T" "V" "F" "R" "T" "L" "K" "A" "L" "Y"
[199] "K" "T" "H" "A" "C" "Y" "E" "H" "N" "H" "I" "F" "P" "L" "L" "E" "K" "Y"
[217] "C" "G" "F" "R" "E" "D" "N" "I" "P" "Q" "L" "E" "D" "V" "S" "Q" "F" "L"
[235] "Q" "T" "C" "T" "G" "F" "R" "L" "R" "P" "V" "A" "G" "L" "L" "S" "S" "R"
[253] "D" "F" "L" "G" "G" "L" "A" "F" "R" "V" "F" "H" "C" "T" "Q" "Y" "I" "R"
[271] "H" "G" "S" "K" "P" "M" "Y" "T" "P" "E" "P" "D" "I" "C" "H" "E" "L" "L"
[289] "G" "H" "V" "P" "L" "F" "S" "D" "R" "S" "F" "A" "Q" "F" "S" "Q" "E" "I"
[307] "G" "-" "L" "A" "S" "L" "G" "A" "P" "D" "E" "Y" "I" "E" "K" "L" "A" "T"
[325] "I" "Y" "W" "F" "T" "V" "E" "F" "G" "L" "C" "K" "E" "G" "-" "D" "S" "I"
[343] "K" "A" "Y" "G" "A" "G" "L" "L" "S" "S" "F" "G" "E" "L" "Q" "Y" "C" "L"
[361] "S" "D" "-" "K" "P" "K" "L" "L" "P" "L" "E" "L" "E" "K" "T" "A" "C" "Q"
[379] "E" "Y" "S" "V" "T" "E" "F" "Q" "P" "L" "Y" "Y" "V" "A" "E" "S" "F" "S"
[397] "D" "A" "K" "E" "K" "V" "R" "T" "F" "A" "A" "T" "I" "P" "R" "P" "F" "S"
[415] "V" "R" "Y" "D" "P" "Y" "T" "Q" "R" "V" "E" "V" "L" "D" "N" "T" "Q" "Q"
[433] "L" "K" "I" "L" "A" "D" "S" "I" "N" "S" "E" "V" "G" "I" "L" "C" "N" "A"
[451] "L" "Q" "K" "I" "K" "S"

$PH4H_Mus_musculus
  [1] "M" "A" "A" "V" "V" "L" "E" "N" "G" "V" "L" "S" "R" "K" "L" "S" "D" "F"
 [19] "G" "Q" "E" "T" "S" "Y" "I" "E" "D" "N" "S" "N" "Q" "N" "G" "A" "V" "S"
 [37] "L" "I" "F" "S" "L" "K" "E" "E" "V" "G" "A" "L" "A" "K" "V" "L" "R" "L"
 [55] "F" "E" "E" "N" "E" "I" "N" "L" "T" "H" "I" "E" "S" "R" "P" "S" "R" "L"
 [73] "N" "K" "D" "E" "Y" "E" "F" "F" "T" "Y" "L" "D" "K" "R" "S" "K" "P" "V"
 [91] "L" "G" "S" "I" "I" "K" "S" "L" "R" "N" "D" "I" "G" "A" "T" "V" "H" "E"
[109] "L" "S" "R" "D" "K" "E" "K" "N" "T" "V" "P" "W" "F" "P" "R" "T" "I" "Q"
[127] "E" "L" "D" "R" "F" "A" "N" "Q" "I" "L" "S" "Y" "G" "A" "E" "L" "D" "A"
[145] "D" "H" "P" "G" "F" "K" "D" "P" "V" "Y" "R" "A" "R" "R" "K" "Q" "F" "A"
[163] "D" "I" "A" "Y" "N" "Y" "R" "H" "G" "Q" "P" "I" "P" "R" "V" "E" "Y" "T"
[181] "E" "E" "E" "R" "K" "T" "W" "G" "T" "V" "F" "R" "T" "L" "K" "A" "L" "Y"
[199] "K" "T" "H" "A" "C" "Y" "E" "H" "N" "H" "I" "F" "P" "L" "L" "E" "K" "Y"
[217] "C" "G" "F" "R" "E" "D" "N" "I" "P" "Q" "L" "E" "D" "V" "S" "Q" "F" "L"
[235] "Q" "T" "C" "T" "G" "F" "R" "L" "R" "P" "V" "A" "G" "L" "L" "S" "S" "R"
[253] "D" "F" "L" "G" "G" "L" "A" "F" "R" "V" "F" "H" "C" "T" "Q" "Y" "I" "R"
[271] "H" "G" "S" "K" "P" "M" "Y" "T" "P" "E" "P" "D" "I" "C" "H" "E" "L" "L"
[289] "G" "H" "V" "P" "L" "F" "S" "D" "R" "S" "F" "A" "Q" "F" "S" "Q" "E" "I"
[307] "G" "-" "L" "A" "S" "L" "G" "A" "P" "D" "E" "Y" "I" "E" "K" "L" "A" "T"
[325] "I" "Y" "W" "F" "T" "V" "E" "F" "G" "L" "C" "K" "E" "G" "-" "D" "S" "I"
[343] "K" "A" "Y" "G" "A" "G" "L" "L" "S" "S" "F" "G" "E" "L" "Q" "Y" "C" "L"
[361] "S" "D" "-" "K" "P" "K" "L" "L" "P" "L" "E" "L" "E" "K" "T" "A" "C" "Q"
[379] "E" "Y" "T" "V" "T" "E" "F" "Q" "P" "L" "Y" "Y" "V" "A" "E" "S" "F" "N"
[397] "D" "A" "K" "E" "K" "V" "R" "T" "F" "A" "A" "T" "I" "P" "R" "P" "F" "S"
[415] "V" "R" "Y" "D" "P" "Y" "T" "Q" "R" "V" "E" "V" "L" "D" "N" "T" "Q" "Q"
[433] "L" "K" "I" "L" "A" "D" "S" "I" "N" "S" "E" "V" "G" "I" "L" "C" "H" "A"
[451] "L" "Q" "K" "I" "K" "S"

$PH4H_Homo_sapiens
  [1] "M" "S" "T" "A" "V" "L" "E" "N" "P" "G" "L" "G" "R" "K" "L" "S" "D" "F"
 [19] "G" "Q" "E" "T" "S" "Y" "I" "E" "D" "N" "C" "N" "Q" "N" "G" "A" "I" "S"
 [37] "L" "I" "F" "S" "L" "K" "E" "E" "V" "G" "A" "L" "A" "K" "V" "L" "R" "L"
 [55] "F" "E" "E" "N" "D" "V" "N" "L" "T" "H" "I" "E" "S" "R" "P" "S" "R" "L"
 [73] "K" "K" "D" "E" "Y" "E" "F" "F" "T" "H" "L" "D" "K" "R" "S" "L" "P" "A"
 [91] "L" "T" "N" "I" "I" "K" "I" "L" "R" "H" "D" "I" "G" "A" "T" "V" "H" "E"
[109] "L" "S" "R" "D" "K" "K" "K" "D" "T" "V" "P" "W" "F" "P" "R" "T" "I" "Q"
[127] "E" "L" "D" "R" "F" "A" "N" "Q" "I" "L" "S" "Y" "G" "A" "E" "L" "D" "A"
[145] "D" "H" "P" "G" "F" "K" "D" "P" "V" "Y" "R" "A" "R" "R" "K" "Q" "F" "A"
[163] "D" "I" "A" "Y" "N" "Y" "R" "H" "G" "Q" "P" "I" "P" "R" "V" "E" "Y" "M"
[181] "E" "E" "E" "K" "K" "T" "W" "G" "T" "V" "F" "K" "T" "L" "K" "S" "L" "Y"
[199] "K" "T" "H" "A" "C" "Y" "E" "Y" "N" "H" "I" "F" "P" "L" "L" "E" "K" "Y"
[217] "C" "G" "F" "H" "E" "D" "N" "I" "P" "Q" "L" "E" "D" "V" "S" "Q" "F" "L"
[235] "Q" "T" "C" "T" "G" "F" "R" "L" "R" "P" "V" "A" "G" "L" "L" "S" "S" "R"
[253] "D" "F" "L" "G" "G" "L" "A" "F" "R" "V" "F" "H" "C" "T" "Q" "Y" "I" "R"
[271] "H" "G" "S" "K" "P" "M" "Y" "T" "P" "E" "P" "D" "I" "C" "H" "E" "L" "L"
[289] "G" "H" "V" "P" "L" "F" "S" "D" "R" "S" "F" "A" "Q" "F" "S" "Q" "E" "I"
[307] "G" "-" "L" "A" "S" "L" "G" "A" "P" "D" "E" "Y" "I" "E" "K" "L" "A" "T"
[325] "I" "Y" "W" "F" "T" "V" "E" "F" "G" "L" "C" "K" "Q" "G" "-" "D" "S" "I"
[343] "K" "A" "Y" "G" "A" "G" "L" "L" "S" "S" "F" "G" "E" "L" "Q" "Y" "C" "L"
[361] "S" "E" "-" "K" "P" "K" "L" "L" "P" "L" "E" "L" "E" "K" "T" "A" "I" "Q"
[379] "N" "Y" "T" "V" "T" "E" "F" "Q" "P" "L" "Y" "Y" "V" "A" "E" "S" "F" "N"
[397] "D" "A" "K" "E" "K" "V" "R" "N" "F" "A" "A" "T" "I" "P" "R" "P" "F" "S"
[415] "V" "R" "Y" "D" "P" "Y" "T" "Q" "R" "I" "E" "V" "L" "D" "N" "T" "Q" "Q"
[433] "L" "K" "I" "L" "A" "D" "S" "I" "N" "S" "E" "I" "G" "I" "L" "C" "S" "A"
[451] "L" "Q" "K" "I" "K" "-"

$PH4H_Bos_taurus
  [1] "M" "S" "A" "L" "V" "L" "E" "S" "R" "A" "L" "G" "R" "K" "L" "S" "D" "F"
 [19] "G" "Q" "E" "T" "S" "Y" "I" "E" "G" "N" "S" "D" "Q" "N" "-" "A" "V" "S"
 [37] "L" "I" "F" "S" "L" "K" "E" "E" "V" "G" "A" "L" "A" "R" "V" "L" "R" "L"
 [55] "F" "E" "E" "N" "D" "I" "N" "L" "T" "H" "I" "E" "S" "R" "P" "S" "R" "L"
 [73] "R" "K" "D" "E" "Y" "E" "F" "F" "T" "N" "L" "D" "Q" "R" "S" "V" "P" "A"
 [91] "L" "A" "N" "I" "I" "K" "I" "L" "R" "H" "D" "I" "G" "A" "T" "V" "H" "E"
[109] "L" "S" "R" "D" "K" "K" "K" "D" "T" "V" "P" "W" "F" "P" "R" "T" "I" "Q"
[127] "E" "L" "D" "N" "F" "A" "N" "Q" "V" "L" "S" "Y" "G" "A" "E" "L" "D" "A"
[145] "D" "H" "P" "G" "F" "K" "D" "P" "V" "Y" "R" "A" "R" "R" "K" "Q" "F" "A"
[163] "D" "I" "A" "Y" "N" "Y" "R" "H" "G" "Q" "P" "I" "P" "R" "V" "E" "Y" "T"
[181] "E" "E" "E" "K" "K" "T" "W" "G" "T" "V" "F" "R" "T" "L" "K" "S" "L" "Y"
[199] "K" "T" "H" "A" "C" "Y" "E" "H" "N" "H" "I" "F" "P" "L" "L" "E" "K" "Y"
[217] "C" "G" "F" "R" "E" "D" "N" "I" "P" "Q" "L" "E" "E" "V" "S" "Q" "F" "L"
[235] "Q" "S" "C" "T" "G" "F" "R" "L" "R" "P" "V" "A" "G" "L" "L" "S" "S" "R"
[253] "D" "F" "L" "G" "G" "L" "A" "F" "R" "V" "F" "H" "C" "T" "Q" "Y" "I" "R"
[271] "H" "G" "S" "K" "P" "M" "Y" "T" "P" "E" "P" "D" "I" "C" "H" "E" "L" "L"
[289] "G" "H" "V" "P" "L" "F" "S" "D" "R" "S" "F" "A" "Q" "F" "S" "Q" "E" "I"
[307] "G" "-" "L" "A" "S" "L" "G" "A" "P" "D" "E" "Y" "I" "E" "K" "L" "A" "T"
[325] "I" "Y" "W" "F" "T" "V" "E" "F" "G" "L" "C" "K" "Q" "G" "-" "D" "S" "I"
[343] "K" "A" "Y" "G" "A" "G" "L" "L" "S" "S" "F" "G" "E" "L" "Q" "Y" "C" "L"
[361] "S" "D" "-" "K" "P" "K" "L" "L" "P" "L" "E" "L" "E" "K" "T" "A" "V" "Q"
[379] "E" "Y" "T" "I" "T" "E" "F" "Q" "P" "L" "Y" "Y" "V" "A" "E" "S" "F" "N"
[397] "D" "A" "K" "E" "K" "V" "R" "N" "F" "A" "A" "T" "I" "P" "R" "P" "F" "S"
[415] "V" "H" "Y" "D" "P" "Y" "T" "Q" "R" "I" "E" "V" "L" "D" "N" "T" "Q" "Q"
[433] "L" "K" "I" "L" "A" "D" "S" "I" "S" "S" "E" "V" "E" "I" "L" "C" "S" "A"
[451] "L" "Q" "K" "L" "K" "-"

$PH4H_Chromobacterium_violaceum
  [1] "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-"
 [19] "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-"
 [37] "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-"
 [55] "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-"
 [73] "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-"
 [91] "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-"
[109] "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-"
[127] "-" "-" "-" "-" "-" "-" "M" "N" "D" "R" "A" "D" "F" "V" "V" "P" "D" "-"
[145] "-" "-" "-" "-" "I" "T" "T" "R" "K" "N" "V" "G" "L" "S" "H" "D" "A" "N"
[163] "-" "-" "-" "-" "-" "-" "D" "F" "T" "L" "P" "Q" "P" "L" "D" "R" "Y" "S"
[181] "A" "E" "D" "H" "A" "T" "W" "A" "T" "L" "Y" "Q" "R" "Q" "C" "K" "L" "L"
[199] "P" "G" "R" "A" "C" "D" "E" "F" "M" "E" "G" "L" "-" "-" "-" "-" "E" "R"
[217] "L" "E" "V" "D" "A" "D" "R" "V" "P" "D" "F" "N" "K" "L" "N" "Q" "K" "L"
[235] "M" "A" "A" "T" "G" "W" "K" "I" "V" "A" "V" "P" "G" "L" "I" "P" "D" "D"
[253] "V" "F" "F" "E" "H" "L" "A" "N" "R" "R" "F" "P" "V" "T" "W" "W" "L" "R"
[271] "E" "P" "H" "Q" "L" "D" "Y" "L" "Q" "E" "P" "D" "V" "F" "H" "D" "L" "F"
[289] "G" "H" "V" "P" "L" "L" "I" "N" "P" "V" "F" "A" "D" "Y" "L" "E" "A" "Y"
[307] "G" "K" "G" "G" "V" "K" "A" "K" "A" "L" "G" "A" "L" "P" "M" "L" "A" "R"
[325] "L" "Y" "W" "Y" "T" "V" "E" "F" "G" "L" "I" "N" "T" "P" "-" "A" "G" "M"
[343] "R" "I" "Y" "G" "A" "G" "I" "L" "S" "S" "K" "S" "E" "S" "I" "Y" "C" "L"
[361] "D" "S" "A" "S" "P" "N" "R" "V" "G" "F" "D" "L" "M" "R" "I" "M" "N" "T"
[379] "R" "Y" "R" "I" "D" "T" "F" "Q" "K" "T" "Y" "F" "V" "I" "D" "S" "F" "K"
[397] "Q" "L" "F" "D" "A" "T" "A" "-" "P" "D" "F" "A" "P" "L" "Y" "L" "Q" "L"
[415] "A" "D" "A" "Q" "P" "W" "G" "A" "G" "D" "V" "A" "P" "D" "D" "L" "V" "L"
[433] "N" "A" "G" "D" "R" "Q" "G" "W" "A" "D" "T" "E" "D" "V" "-" "-" "-" "-"
[451] "-" "-" "-" "-" "-" "-"

$PH4H_Ralstonia_solanacearum
  [1] "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-"
 [19] "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-"
 [37] "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-"
 [55] "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-"
 [73] "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-"
 [91] "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-"
[109] "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-"
[127] "-" "M" "A" "I" "A" "T" "P" "T" "S" "A" "A" "P" "T" "P" "A" "P" "A" "G"
[145] "F" "T" "G" "T" "L" "T" "D" "K" "L" "R" "E" "Q" "F" "A" "E" "G" "L" "D"
[163] "G" "Q" "T" "L" "R" "P" "D" "F" "T" "M" "E" "Q" "P" "V" "H" "R" "Y" "T"
[181] "A" "A" "D" "H" "A" "T" "W" "R" "T" "L" "Y" "D" "R" "Q" "E" "A" "L" "L"
[199] "P" "G" "R" "A" "C" "D" "E" "F" "L" "Q" "G" "L" "-" "-" "-" "-" "S" "T"
[217] "L" "G" "M" "S" "R" "E" "G" "V" "P" "S" "F" "D" "R" "L" "N" "E" "T" "L"
[235] "M" "R" "A" "T" "G" "W" "Q" "I" "V" "A" "V" "P" "G" "L" "V" "P" "D" "E"
[253] "V" "F" "F" "E" "H" "L" "A" "N" "R" "R" "F" "P" "A" "S" "W" "W" "M" "R"
[271] "R" "P" "D" "Q" "L" "D" "Y" "L" "Q" "E" "P" "D" "G" "F" "H" "D" "I" "F"
[289] "G" "H" "V" "P" "L" "L" "I" "N" "P" "V" "F" "A" "D" "Y" "M" "Q" "A" "Y"
[307] "G" "Q" "G" "G" "L" "K" "A" "A" "R" "L" "G" "A" "L" "D" "M" "L" "A" "R"
[325] "L" "Y" "W" "Y" "T" "V" "E" "F" "G" "L" "I" "R" "T" "P" "-" "A" "G" "L"
[343] "R" "I" "Y" "G" "A" "G" "I" "V" "S" "S" "K" "S" "E" "S" "V" "Y" "A" "L"
[361] "D" "S" "A" "S" "P" "N" "R" "I" "G" "F" "D" "V" "H" "R" "I" "M" "R" "T"
[379] "R" "Y" "R" "I" "D" "T" "F" "Q" "K" "T" "Y" "F" "V" "I" "D" "S" "F" "E"
[397] "Q" "L" "F" "D" "A" "T" "R" "-" "P" "D" "F" "T" "P" "L" "Y" "E" "A" "L"
[415] "G" "T" "L" "P" "T" "F" "G" "A" "G" "D" "V" "V" "D" "G" "D" "A" "V" "L"
[433] "N" "A" "G" "T" "R" "E" "G" "W" "A" "D" "T" "A" "D" "I" "-" "-" "-" "-"
[451] "-" "-" "-" "-" "-" "-"

$PH4H_Caulobacter_crescentus
  [1] "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-"
 [19] "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-"
 [37] "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-"
 [55] "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-"
 [73] "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-"
 [91] "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-"
[109] "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-"
[127] "-" "-" "-" "-" "-" "-" "M" "S" "G" "-" "-" "-" "-" "-" "-" "-" "-" "-"
[145] "-" "-" "-" "-" "-" "-" "D" "G" "L" "S" "N" "G" "P" "P" "P" "G" "A" "R"
[163] "-" "-" "-" "-" "-" "P" "D" "W" "T" "I" "D" "Q" "G" "W" "E" "T" "Y" "T"
[181] "Q" "A" "E" "H" "D" "V" "W" "I" "T" "L" "Y" "E" "R" "Q" "T" "D" "M" "L"
[199] "H" "G" "R" "A" "C" "D" "E" "F" "M" "R" "G" "L" "-" "-" "-" "-" "D" "A"
[217] "L" "D" "L" "H" "R" "S" "G" "I" "P" "D" "F" "A" "R" "I" "N" "E" "E" "L"
[235] "K" "R" "L" "T" "G" "W" "T" "V" "V" "A" "V" "P" "G" "L" "V" "P" "D" "D"
[253] "V" "F" "F" "D" "H" "L" "A" "N" "R" "R" "F" "P" "A" "G" "Q" "F" "I" "R"
[271] "K" "P" "H" "E" "L" "D" "Y" "L" "Q" "E" "P" "D" "I" "F" "H" "D" "V" "F"
[289] "G" "H" "V" "P" "M" "L" "T" "D" "P" "V" "F" "A" "D" "Y" "M" "Q" "A" "Y"
[307] "G" "E" "G" "G" "R" "R" "A" "L" "G" "L" "G" "R" "L" "A" "N" "L" "A" "R"
[325] "L" "Y" "W" "Y" "T" "V" "E" "F" "G" "L" "M" "N" "T" "P" "-" "A" "G" "L"
[343] "R" "I" "Y" "G" "A" "G" "I" "V" "S" "S" "R" "T" "E" "S" "I" "F" "A" "L"
[361] "D" "D" "P" "S" "P" "N" "R" "I" "G" "F" "D" "L" "E" "R" "V" "M" "R" "T"
[379] "L" "Y" "R" "I" "D" "D" "F" "Q" "Q" "V" "Y" "F" "V" "I" "D" "S" "I" "Q"
[397] "T" "L" "Q" "E" "V" "T" "L" "-" "R" "D" "F" "G" "A" "I" "Y" "E" "R" "L"
[415] "A" "S" "V" "S" "D" "I" "G" "V" "A" "E" "I" "V" "P" "G" "D" "A" "V" "L"
[433] "T" "R" "G" "T" "-" "Q" "A" "Y" "A" "T" "A" "G" "G" "R" "L" "A" "G" "A"
[451] "A" "A" "G" "-" "-" "-"

$PH4H_Pseudomonas_aeruginosa
  [1] "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-"
 [19] "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-"
 [37] "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-"
 [55] "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-"
 [73] "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-"
 [91] "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-"
[109] "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-"
[127] "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-"
[145] "-" "-" "-" "-" "-" "-" "M" "K" "T" "T" "Q" "Y" "V" "A" "R" "Q" "P" "D"
[163] "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "D" "N" "G" "F" "I" "H" "Y" "P"
[181] "E" "T" "E" "H" "Q" "V" "W" "N" "T" "L" "I" "T" "R" "Q" "L" "K" "V" "I"
[199] "E" "G" "R" "A" "C" "Q" "E" "Y" "L" "D" "G" "I" "-" "-" "-" "-" "E" "Q"
[217] "L" "G" "L" "P" "H" "E" "R" "I" "P" "Q" "L" "D" "E" "I" "N" "R" "V" "L"
[235] "Q" "A" "T" "T" "G" "W" "R" "V" "A" "R" "V" "P" "A" "L" "I" "P" "F" "Q"
[253] "T" "F" "F" "E" "L" "L" "A" "S" "Q" "Q" "F" "P" "V" "A" "T" "F" "I" "R"
[271] "T" "P" "E" "E" "L" "D" "Y" "L" "Q" "E" "P" "D" "I" "F" "H" "E" "I" "F"
[289] "G" "H" "C" "P" "L" "L" "T" "N" "P" "W" "F" "A" "E" "F" "T" "H" "T" "Y"
[307] "G" "K" "L" "G" "L" "K" "A" "S" "K" "E" "-" "E" "R" "V" "F" "L" "A" "R"
[325] "L" "Y" "W" "M" "T" "I" "E" "F" "G" "L" "V" "E" "T" "D" "-" "Q" "G" "K"
[343] "R" "I" "Y" "G" "G" "G" "I" "L" "S" "S" "P" "K" "E" "T" "V" "Y" "S" "L"
[361] "S" "D" "-" "E" "P" "L" "H" "Q" "A" "F" "N" "P" "L" "E" "A" "M" "R" "T"
[379] "P" "Y" "R" "I" "D" "I" "L" "Q" "P" "L" "Y" "F" "V" "L" "P" "D" "L" "K"
[397] "R" "L" "F" "Q" "L" "A" "Q" "-" "E" "D" "I" "M" "A" "L" "V" "H" "E" "A"
[415] "M" "R" "L" "G" "-" "L" "H" "A" "P" "L" "F" "P" "P" "K" "Q" "A" "A" "-"
[433] "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-"
[451] "-" "-" "-" "-" "-" "-"

$PH4H_Rhizobium_loti
  [1] "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-"
 [19] "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-"
 [37] "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-"
 [55] "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-"
 [73] "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-"
 [91] "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-"
[109] "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-"
[127] "-" "-" "-" "-" "-" "-" "M" "S" "V" "A" "E" "Y" "A" "R" "-" "-" "-" "-"
[145] "-" "-" "-" "-" "-" "-" "D" "C" "A" "A" "Q" "G" "L" "R" "G" "D" "Y" "S"
[163] "-" "-" "V" "C" "R" "A" "D" "F" "T" "V" "A" "Q" "D" "Y" "D" "-" "Y" "S"
[181] "D" "E" "E" "Q" "A" "V" "W" "R" "T" "L" "C" "D" "R" "Q" "T" "K" "L" "T"
[199] "R" "K" "L" "A" "H" "H" "S" "Y" "L" "D" "G" "V" "-" "-" "-" "-" "E" "K"
[217] "L" "G" "L" "-" "L" "D" "R" "I" "P" "D" "F" "E" "D" "V" "S" "T" "K" "L"
[235] "R" "K" "L" "T" "G" "W" "E" "I" "I" "A" "V" "P" "G" "L" "I" "P" "A" "A"
[253] "P" "F" "F" "D" "H" "L" "A" "N" "R" "R" "F" "P" "V" "T" "N" "W" "L" "R"
[271] "T" "R" "Q" "E" "L" "D" "Y" "I" "V" "E" "P" "D" "M" "F" "H" "D" "F" "F"
[289] "G" "H" "V" "P" "V" "L" "S" "Q" "P" "V" "F" "A" "D" "F" "M" "Q" "M" "Y"
[307] "G" "K" "K" "A" "G" "D" "I" "I" "A" "L" "G" "G" "D" "E" "M" "I" "T" "R"
[325] "L" "Y" "W" "Y" "T" "A" "E" "Y" "G" "L" "V" "Q" "E" "A" "G" "Q" "P" "L"
[343] "K" "A" "F" "G" "A" "G" "L" "M" "S" "S" "F" "T" "E" "L" "Q" "F" "A" "V"
[361] "E" "G" "K" "D" "A" "H" "H" "V" "P" "F" "D" "L" "E" "T" "V" "M" "R" "T"
[379] "G" "Y" "E" "I" "D" "K" "F" "Q" "R" "A" "Y" "F" "V" "L" "P" "S" "F" "D"
[397] "A" "L" "R" "D" "A" "F" "Q" "T" "A" "D" "F" "E" "A" "I" "V" "A" "R" "R"
[415] "K" "D" "Q" "K" "A" "L" "D" "P" "A" "T" "V" "-" "-" "-" "-" "-" "-" "-"
[433] "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-" "-"
[451] "-" "-" "-" "-" "-" "-"

attr(,"class")
[1] "align"

msa documentation built on Nov. 17, 2017, 8:22 a.m.