msaConvert: Convert Multiple Sequence Alignment for Other Packages
In msa: Multiple Sequence Alignment
Description
Usage
Arguments
Details
Value
Author(s)
References
See Also
Examples
Description
This function converts a multiple sequence alignment object
to formats used in other sequence analysis packages.
Usage
1
2
3
4
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 <msa@bioinf.jku.at>
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
1
2
3
4
5
6
7
8
9
10
11
12
## 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. 8, 2020, 5:41 p.m.
R Package Documentation
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Description Usage Arguments Details Value Author(s) References See Also Examples
Description
This function converts a multiple sequence alignment object to formats used in other sequence analysis packages.
Usage
1 2 3 4 | msaConvert(x,
type=c("seqinr::alignment", "bios2mds::align",
"ape::AAbin", "ape::DNAbin",
"phangorn::phyDat", "bio3d::fasta"))
|
Arguments
x |
an object of class |
type |
a character string specifying to which type of object
|
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 <msa@bioinf.jku.at>
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
1 2 3 4 5 6 7 8 9 10 11 12 | ## 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"
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