README.md
In DomBennett/om..trimal: Outsider module for running trimal
Run trimal with outsider in R
TRIMAL: Automated removal of spurious sequences or poorly aligned
regions from a multiple sequence alignment
Install and look up help
library(outsider)
#> ----------------
#> outsider v 0.1.0
#> ----------------
#> - Security notice: be sure of which modules you install
module_install(repo = "dombennett/om..trimal")
#> -----------------------------------------------------
#> Warning: You are about to install an outsider module!
#> -----------------------------------------------------
#> Outsider modules install and run external programs
#> via Docker <https://www.docker.com>. These external
#> programs may communicate with the internet and could
#> potentially be malicious.
#>
#> Be sure to know the module you are about to install:
#> Is it from a trusted developer? Are colleagues using
#> it? Is it supposed to download lots of data? Is it
#> well used (e.g. check number of stars on GitHub)?
#> -----------------------------------------------------
#> Module information
#> -----------------------------------------------------
#> program: trimal
#> details: A tool for automated alignment trimming in large-scale phylogenetic analyses.
#> docker: dombennett
#> github: dombennett
#> url: https://github.com/DomBennett/om..trimal
#> image: dombennett/om_trimal
#> container: om_trimal
#> package: om..trimal
#> Travis CI: Passing
#> -----------------------------------------------------
#> Enter any key to continue or press Esc to quit
#module_help(repo = "dombennett/om..trimal")
The module provides two functions trimal, the main program for
trimming alignments, and readal, a convenience tool for converting
alignments into different file formats.
Examples
Both functions have two arguments:
arglist: character vector of arguments to be passed to the programoutdir: File location where all resulting files will be returned
The arglist function must be a character vector. For example, a call
to a command-line program, like …
command -xarg file --yarg --zarg=p1
Would be in R …
command(arglist=c('-xarg', file, '--yarg', '--zarg=p1'))
All the arguments indicated with the -h flag for both trimal and
readal can be specified in the above way.
trimal
library(outsider)
# import
trimal <- module_import('trimal', repo = 'dombennett/om..trimal')
# help
trimal('-h')
#>
#> trimAl v1.4.rev22 build[2015-05-21]. 2009-2015. Salvador Capella-Gutierrez and Toni Gabaldón.
#>
#> trimAl webpage: http://trimal.cgenomics.org
#>
#> This program is free software: you can redistribute it and/or modify
#> it under the terms of the GNU General Public License as published by
#> the Free Software Foundation, the last available version.
#>
#> Please cite:
#> trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses.
#> Salvador Capella-Gutierrez; Jose M. Silla-Martinez; Toni Gabaldon.
#> Bioinformatics 2009, 25:1972-1973.
#>
#> Basic usage
#> trimal -in <inputfile> -out <outputfile> -(other options).
#>
#> Common options (for a complete list please see the User Guide or visit http://trimal.cgenomics.org):
#>
#> -h Print this information and show some examples.
#> --version Print the trimAl version.
#>
#> -in <inputfile> Input file in several formats (clustal, fasta, NBRF/PIR, nexus, phylip3.2, phylip).
#>
#> -compareset <inputfile> Input list of paths for the files containing the alignments to compare.
#> -forceselect <inputfile> Force selection of the given input file in the files comparison method.
#>
#> -backtrans <inputfile> Use a Coding Sequences file to get a backtranslation for a given AA alignment
#> -ignorestopcodon Ignore stop codons in the input coding sequences
#> -splitbystopcodon Split input coding sequences up to first stop codon appearance
#>
#> -matrix <inpufile> Input file for user-defined similarity matrix (default is Blosum62).
#> --alternative_matrix <name> Select an alternative similarity matrix already loaded.
#> Only available 'degenerated_nt_identity'
#>
#> -out <outputfile> Output alignment in the same input format (default stdout). (default input format)
#> -htmlout <outputfile> Get a summary of trimal's work in an HTML file.
#>
#> -keepheader Keep original sequence header including non-alphanumeric characters.
#> Only available for input FASTA format files. (future versions will extend this feature)
#>
#> -nbrf Output file in NBRF/PIR format
#> -mega Output file in MEGA format
#> -nexus Output file in NEXUS format
#> -clustal Output file in CLUSTAL format
#>
#> -fasta Output file in FASTA format
#> -fasta_m10 Output file in FASTA format. Sequences name length up to 10 characters.
#>
#> -phylip Output file in PHYLIP/PHYLIP4 format
#> -phylip_m10 Output file in PHYLIP/PHYLIP4 format. Sequences name length up to 10 characters.
#> -phylip_paml Output file in PHYLIP format compatible with PAML
#> -phylip_paml_m10 Output file in PHYLIP format compatible with PAML. Sequences name length up to 10 characters.
#> -phylip3.2 Output file in PHYLIP3.2 format
#> -phylip3.2_m10 Output file in PHYLIP3.2 format. Sequences name length up to 10 characters.
#>
#> -complementary Get the complementary alignment.
#> -colnumbering Get the relationship between the columns in the old and new alignment.
#>
#> -selectcols { n,l,m-k } Selection of columns to be removed from the alignment. Range: [0 - (Number of Columns - 1)]. (see User Guide).
#> -selectseqs { n,l,m-k } Selection of sequences to be removed from the alignment. Range: [0 - (Number of Sequences - 1)]. (see User Guide).
#>
#> -gt -gapthreshold <n> 1 - (fraction of sequences with a gap allowed). Range: [0 - 1]
#> -st -simthreshold <n> Minimum average similarity allowed. Range: [0 - 1]
#> -ct -conthreshold <n> Minimum consistency value allowed.Range: [0 - 1]
#> -cons <n> Minimum percentage of the positions in the original alignment to conserve. Range: [0 - 100]
#>
#> -nogaps Remove all positions with gaps in the alignment.
#> -noallgaps Remove columns composed only by gaps.
#> -keepseqs Keep sequences even if they are composed only by gaps.
#>
#> -gappyout Use automated selection on "gappyout" mode. This method only uses information based on gaps' distribution. (see User Guide).
#> -strict Use automated selection on "strict" mode. (see User Guide).
#> -strictplus Use automated selection on "strictplus" mode. (see User Guide).
#> (Optimized for Neighbour Joining phylogenetic tree reconstruction).
#>
#> -automated1 Use a heuristic selection of the automatic method based on similarity statistics. (see User Guide). (Optimized for Maximum Likelihood phylogenetic tree reconstruction).
#>
#> -terminalonly Only columns out of internal boundaries (first and last column without gaps) are
#> candidates to be trimmed depending on the selected method
#> --set_boundaries { l,r } Set manually left (l) and right (r) boundaries - only columns out of these boundaries are
#> candidates to be trimmed depending on the selected method. Range: [0 - (Number of Columns - 1)]
#> -block <n> Minimum column block size to be kept in the trimmed alignment. Available with manual and automatic (gappyout) methods
#>
#> -resoverlap Minimum overlap of a positions with other positions in the column to be considered a "good position". Range: [0 - 1]. (see User Guide).
#> -seqoverlap Minimum percentage of "good positions" that a sequence must have in order to be conserved. Range: [0 - 100](see User Guide).
#>
#> -clusters <n> Get the most Nth representatives sequences from a given alignment. Range: [1 - (Number of sequences)]
#> -maxidentity <n> Get the representatives sequences for a given identity threshold. Range: [0 - 1].
#>
#> -w <n> (half) Window size, score of position i is the average of the window (i - n) to (i + n).
#> -gw <n> (half) Window size only applies to statistics/methods based on Gaps.
#> -sw <n> (half) Window size only applies to statistics/methods based on Similarity.
#> -cw <n> (half) Window size only applies to statistics/methods based on Consistency.
#>
#> -sgc Print gap scores for each column in the input alignment.
#> -sgt Print accumulated gap scores for the input alignment.
#> -ssc Print similarity scores for each column in the input alignment.
#> -sst Print accumulated similarity scores for the input alignment.
#> -sfc Print sum-of-pairs scores for each column from the selected alignment
#> -sft Print accumulated sum-of-pairs scores for the selected alignment
#> -sident Print identity scores matrix for all sequences in the input alignment. (see User Guide).
#> -soverlap Print overlap scores matrix for all sequences in the input alignment. (see User Guide).
#>
#> Some Examples:
#>
#> 1) Removes all positions in the alignment with gaps in 10% or more of
#> the sequences, unless this leaves less than 60% of original alignment.
#> In such case, print the 60% best (with less gaps) positions.
#>
#> trimal -in <inputfile> -out <outputfile> -gt 0.9 -cons 60
#>
#> 2) As above but, the gap score is averaged over a window starting
#> 3 positions before and ending 3 positions after each column.
#>
#> trimal -in <inputfile> -out <outputfile> -gt 0.9 -cons 60 -w 3
#>
#> 3) Use an automatic method to decide optimal thresholds, based in the gap scores
#> from input alignment. (see User Guide for details).
#>
#> trimal -in <inputfile> -out <outputfile> -gappyout
#>
#> 4) Use automatic methods to decide optimal thresholds, based on the combination
#> of gap and similarity scores. (see User Guide for details).
#>
#> trimal -in <inputfile> -out <outputfile> -strictplus
#>
#> 5) Use an heuristic to decide the optimal method for trimming the alignment.
#> (see User Guide for details).
#>
#> trimal -in <inputfile> -out <outputfile> -automated1
#>
#> 6) Use residues and sequences overlap thresholds to delete some sequences from the
#> alignemnt. (see User Guide for details).
#>
#> trimal -in <inputfile> -out <outputfile> -resoverlap 0.8 -seqoverlap 75
#>
#> 7) Selection of columns to be deleted from the alignment. The selection can
#> be a column number or a column number interval. Start from 0
#>
#> trimal -in <inputfile> -out <outputfile> -selectcols { 0,2,3,10,45-60,68,70-78 }
#>
#> 8) Get the complementary alignment from the alignment previously trimmed.
#>
#> trimal -in <inputfile> -out <outputfile> -selectcols { 0,2,3,10,45-60,68,70-78 } -complementary
#>
#> 9) Selection of sequences to be deleted from the alignment. Start in 0
#>
#> trimal -in <inputfile> -out <outputfile> -selectseqs { 2,4,8-12 }
#>
#> 10) Select the 5 most representative sequences from the alignment
#>
#> trimal -in <inputfile> -out <outputfile> -clusters 5
# Real Example
# download
wd <- file.path(tempdir(), 'trimal_example')
if (!dir.exists(wd)) {
dir.create(wd)
}
alignment_file <- file.path(wd, 'example_alignment.fasta')
url <- 'https://raw.githubusercontent.com/DomBennett/om..trimal/master/example_alignment.fasta'
download.file(url = url, destfile = alignment_file)
# run trimal with automated1 method
trimal(arglist = c('-in', alignment_file, '-out', 'trimal_results.fasta',
'-automated1', '-fasta'), outdir = wd)
# verify
list.files(wd)
#> [1] "example_alignment.fasta" "trimal_results.fasta"
readal
library(outsider)
# import
readal <- module_import('readal', repo = 'dombennett/om..trimal')
# help
readal('-h')
#>
#> readAl v1.4.rev22 build[2015-05-21]. 2009-2015. Salvador Capella-Gutierrez and Toni Gabaldón.
#>
#> readAl webpage: http://trimal.cgenomics.org
#>
#> This program is free software: you can redistribute it and/or modify
#> it under the terms of the GNU General Public License as published by
#> the Free Software Foundation, the last available version.
#>
#> Basic usage
#> readal -in <inputfile> -out <outputfile> [options].
#>
#> -h Show this information.
#> --version Show readAl version.
#>
#> -in <inputfile> Input file in several formats.
#> -out <outputfile> Output file name (default STDOUT).
#>
#> -format Print information about input file format and if sequences are aligned or not.
#> -type Print information about biological sequences datatype (e.g. nucleotides:dna, nucleotides:rna, aminoacids, etc)
#> -info Print information about sequences number, average sequence length, max & min sequence length
#>
#> -onlyseqs Generate output with only residues from input file
#>
#> -html Output residues colored according their physicochemical properties. HTML file.
#>
#> -reverse Output the reverse of sequences in input file.
#>
#> -nbrf Output file in NBRF/PIR format
#> -mega Output file in MEGA format
#> -nexus Output file in NEXUS format
#> -clustal Output file in CLUSTAL format
#>
#> -fasta Output file in FASTA format
#> -fasta_m10 Output file in FASTA format. Sequences name up to 10 characters.
#>
#> -phylip Output file in PHYLIP/PHYLIP4 format
#> -phylip_m10 Output file in PHYLIP/PHYLIP4 format. Sequences name up to 10 characters.
#> -phylip_paml Output file in PHYLIP format compatible with PAML
#> -phylip_paml_m10 Output file in PHYLIP format compatible with PAML. Sequences name up to 10 characters.
#> -phylip3.2 Output file in PHYLIP3.2 format
#> -phylip3.2_m10 Output file in PHYLIP3.2 format. Sequences name up to 10 characters.
# Real Example
# download
wd <- file.path(tempdir(), 'readal_example')
if (!dir.exists(wd)) {
dir.create(wd)
}
alignment_file <- file.path(wd, 'example_alignment.fasta')
url <- 'https://raw.githubusercontent.com/DomBennett/om..trimal/master/example_alignment.fasta'
download.file(url = url, destfile = alignment_file)
# get info
readal(arglist = c('-in', alignment_file, '-info'), outdir = wd)
#> ## Input filename 'example_alignment.fasta'
#> ## Total sequences 10
#> ## Alignment length 3161
#> ## Avg. sequence length 2943.8
#> ## Longest seq. name 'M64487_Thermococcus_celer'
#> ## Longest seq. length 3029
#> ## Shortest seq. name 'M32298_Thermoplasma_acidophilum'
#> ## Shortest seq. length 2908
# convert to phylip
readal(arglist = c('-in', alignment_file, '-out', 'example_alignment.phylip',
'-phylip_m10'), outdir = wd)
# verify
list.files(wd)
#> [1] "example_alignment.fasta" "example_alignment.phylip"
Links
Find out more by visiting the trimAL
homepage.
Please cite
- trimAl: a tool for automated alignment trimming in large-scale
phylogenetic analyses. Salvador Capella-Gutierrez; Jose M.
Silla-Martinez; Toni Gabaldon. Bioinformatics 2009 25: 1972-1973.
- Bennett et al. (2020). outsider: Install and run programs, outside
of R, inside of R. Journal of Open Source Software, In
review
An outsider module
Learn more at outsider
website. Want to build your
own module? Check out outsider.devtools
website.
DomBennett/om..trimal documentation built on Jan. 22, 2020, 1:01 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Run trimal with outsider in R
TRIMAL: Automated removal of spurious sequences or poorly aligned regions from a multiple sequence alignment
Install and look up help
library(outsider)
#> ----------------
#> outsider v 0.1.0
#> ----------------
#> - Security notice: be sure of which modules you install
module_install(repo = "dombennett/om..trimal")
#> -----------------------------------------------------
#> Warning: You are about to install an outsider module!
#> -----------------------------------------------------
#> Outsider modules install and run external programs
#> via Docker <https://www.docker.com>. These external
#> programs may communicate with the internet and could
#> potentially be malicious.
#>
#> Be sure to know the module you are about to install:
#> Is it from a trusted developer? Are colleagues using
#> it? Is it supposed to download lots of data? Is it
#> well used (e.g. check number of stars on GitHub)?
#> -----------------------------------------------------
#> Module information
#> -----------------------------------------------------
#> program: trimal
#> details: A tool for automated alignment trimming in large-scale phylogenetic analyses.
#> docker: dombennett
#> github: dombennett
#> url: https://github.com/DomBennett/om..trimal
#> image: dombennett/om_trimal
#> container: om_trimal
#> package: om..trimal
#> Travis CI: Passing
#> -----------------------------------------------------
#> Enter any key to continue or press Esc to quit
#module_help(repo = "dombennett/om..trimal")
The module provides two functions trimal, the main program for
trimming alignments, and readal, a convenience tool for converting
alignments into different file formats.
Examples
Both functions have two arguments:
arglist: character vector of arguments to be passed to the programoutdir: File location where all resulting files will be returned
The arglist function must be a character vector. For example, a call
to a command-line program, like …
command -xarg file --yarg --zarg=p1
Would be in R …
command(arglist=c('-xarg', file, '--yarg', '--zarg=p1'))
All the arguments indicated with the -h flag for both trimal and
readal can be specified in the above way.
trimal
library(outsider)
# import
trimal <- module_import('trimal', repo = 'dombennett/om..trimal')
# help
trimal('-h')
#>
#> trimAl v1.4.rev22 build[2015-05-21]. 2009-2015. Salvador Capella-Gutierrez and Toni Gabaldón.
#>
#> trimAl webpage: http://trimal.cgenomics.org
#>
#> This program is free software: you can redistribute it and/or modify
#> it under the terms of the GNU General Public License as published by
#> the Free Software Foundation, the last available version.
#>
#> Please cite:
#> trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses.
#> Salvador Capella-Gutierrez; Jose M. Silla-Martinez; Toni Gabaldon.
#> Bioinformatics 2009, 25:1972-1973.
#>
#> Basic usage
#> trimal -in <inputfile> -out <outputfile> -(other options).
#>
#> Common options (for a complete list please see the User Guide or visit http://trimal.cgenomics.org):
#>
#> -h Print this information and show some examples.
#> --version Print the trimAl version.
#>
#> -in <inputfile> Input file in several formats (clustal, fasta, NBRF/PIR, nexus, phylip3.2, phylip).
#>
#> -compareset <inputfile> Input list of paths for the files containing the alignments to compare.
#> -forceselect <inputfile> Force selection of the given input file in the files comparison method.
#>
#> -backtrans <inputfile> Use a Coding Sequences file to get a backtranslation for a given AA alignment
#> -ignorestopcodon Ignore stop codons in the input coding sequences
#> -splitbystopcodon Split input coding sequences up to first stop codon appearance
#>
#> -matrix <inpufile> Input file for user-defined similarity matrix (default is Blosum62).
#> --alternative_matrix <name> Select an alternative similarity matrix already loaded.
#> Only available 'degenerated_nt_identity'
#>
#> -out <outputfile> Output alignment in the same input format (default stdout). (default input format)
#> -htmlout <outputfile> Get a summary of trimal's work in an HTML file.
#>
#> -keepheader Keep original sequence header including non-alphanumeric characters.
#> Only available for input FASTA format files. (future versions will extend this feature)
#>
#> -nbrf Output file in NBRF/PIR format
#> -mega Output file in MEGA format
#> -nexus Output file in NEXUS format
#> -clustal Output file in CLUSTAL format
#>
#> -fasta Output file in FASTA format
#> -fasta_m10 Output file in FASTA format. Sequences name length up to 10 characters.
#>
#> -phylip Output file in PHYLIP/PHYLIP4 format
#> -phylip_m10 Output file in PHYLIP/PHYLIP4 format. Sequences name length up to 10 characters.
#> -phylip_paml Output file in PHYLIP format compatible with PAML
#> -phylip_paml_m10 Output file in PHYLIP format compatible with PAML. Sequences name length up to 10 characters.
#> -phylip3.2 Output file in PHYLIP3.2 format
#> -phylip3.2_m10 Output file in PHYLIP3.2 format. Sequences name length up to 10 characters.
#>
#> -complementary Get the complementary alignment.
#> -colnumbering Get the relationship between the columns in the old and new alignment.
#>
#> -selectcols { n,l,m-k } Selection of columns to be removed from the alignment. Range: [0 - (Number of Columns - 1)]. (see User Guide).
#> -selectseqs { n,l,m-k } Selection of sequences to be removed from the alignment. Range: [0 - (Number of Sequences - 1)]. (see User Guide).
#>
#> -gt -gapthreshold <n> 1 - (fraction of sequences with a gap allowed). Range: [0 - 1]
#> -st -simthreshold <n> Minimum average similarity allowed. Range: [0 - 1]
#> -ct -conthreshold <n> Minimum consistency value allowed.Range: [0 - 1]
#> -cons <n> Minimum percentage of the positions in the original alignment to conserve. Range: [0 - 100]
#>
#> -nogaps Remove all positions with gaps in the alignment.
#> -noallgaps Remove columns composed only by gaps.
#> -keepseqs Keep sequences even if they are composed only by gaps.
#>
#> -gappyout Use automated selection on "gappyout" mode. This method only uses information based on gaps' distribution. (see User Guide).
#> -strict Use automated selection on "strict" mode. (see User Guide).
#> -strictplus Use automated selection on "strictplus" mode. (see User Guide).
#> (Optimized for Neighbour Joining phylogenetic tree reconstruction).
#>
#> -automated1 Use a heuristic selection of the automatic method based on similarity statistics. (see User Guide). (Optimized for Maximum Likelihood phylogenetic tree reconstruction).
#>
#> -terminalonly Only columns out of internal boundaries (first and last column without gaps) are
#> candidates to be trimmed depending on the selected method
#> --set_boundaries { l,r } Set manually left (l) and right (r) boundaries - only columns out of these boundaries are
#> candidates to be trimmed depending on the selected method. Range: [0 - (Number of Columns - 1)]
#> -block <n> Minimum column block size to be kept in the trimmed alignment. Available with manual and automatic (gappyout) methods
#>
#> -resoverlap Minimum overlap of a positions with other positions in the column to be considered a "good position". Range: [0 - 1]. (see User Guide).
#> -seqoverlap Minimum percentage of "good positions" that a sequence must have in order to be conserved. Range: [0 - 100](see User Guide).
#>
#> -clusters <n> Get the most Nth representatives sequences from a given alignment. Range: [1 - (Number of sequences)]
#> -maxidentity <n> Get the representatives sequences for a given identity threshold. Range: [0 - 1].
#>
#> -w <n> (half) Window size, score of position i is the average of the window (i - n) to (i + n).
#> -gw <n> (half) Window size only applies to statistics/methods based on Gaps.
#> -sw <n> (half) Window size only applies to statistics/methods based on Similarity.
#> -cw <n> (half) Window size only applies to statistics/methods based on Consistency.
#>
#> -sgc Print gap scores for each column in the input alignment.
#> -sgt Print accumulated gap scores for the input alignment.
#> -ssc Print similarity scores for each column in the input alignment.
#> -sst Print accumulated similarity scores for the input alignment.
#> -sfc Print sum-of-pairs scores for each column from the selected alignment
#> -sft Print accumulated sum-of-pairs scores for the selected alignment
#> -sident Print identity scores matrix for all sequences in the input alignment. (see User Guide).
#> -soverlap Print overlap scores matrix for all sequences in the input alignment. (see User Guide).
#>
#> Some Examples:
#>
#> 1) Removes all positions in the alignment with gaps in 10% or more of
#> the sequences, unless this leaves less than 60% of original alignment.
#> In such case, print the 60% best (with less gaps) positions.
#>
#> trimal -in <inputfile> -out <outputfile> -gt 0.9 -cons 60
#>
#> 2) As above but, the gap score is averaged over a window starting
#> 3 positions before and ending 3 positions after each column.
#>
#> trimal -in <inputfile> -out <outputfile> -gt 0.9 -cons 60 -w 3
#>
#> 3) Use an automatic method to decide optimal thresholds, based in the gap scores
#> from input alignment. (see User Guide for details).
#>
#> trimal -in <inputfile> -out <outputfile> -gappyout
#>
#> 4) Use automatic methods to decide optimal thresholds, based on the combination
#> of gap and similarity scores. (see User Guide for details).
#>
#> trimal -in <inputfile> -out <outputfile> -strictplus
#>
#> 5) Use an heuristic to decide the optimal method for trimming the alignment.
#> (see User Guide for details).
#>
#> trimal -in <inputfile> -out <outputfile> -automated1
#>
#> 6) Use residues and sequences overlap thresholds to delete some sequences from the
#> alignemnt. (see User Guide for details).
#>
#> trimal -in <inputfile> -out <outputfile> -resoverlap 0.8 -seqoverlap 75
#>
#> 7) Selection of columns to be deleted from the alignment. The selection can
#> be a column number or a column number interval. Start from 0
#>
#> trimal -in <inputfile> -out <outputfile> -selectcols { 0,2,3,10,45-60,68,70-78 }
#>
#> 8) Get the complementary alignment from the alignment previously trimmed.
#>
#> trimal -in <inputfile> -out <outputfile> -selectcols { 0,2,3,10,45-60,68,70-78 } -complementary
#>
#> 9) Selection of sequences to be deleted from the alignment. Start in 0
#>
#> trimal -in <inputfile> -out <outputfile> -selectseqs { 2,4,8-12 }
#>
#> 10) Select the 5 most representative sequences from the alignment
#>
#> trimal -in <inputfile> -out <outputfile> -clusters 5
# Real Example
# download
wd <- file.path(tempdir(), 'trimal_example')
if (!dir.exists(wd)) {
dir.create(wd)
}
alignment_file <- file.path(wd, 'example_alignment.fasta')
url <- 'https://raw.githubusercontent.com/DomBennett/om..trimal/master/example_alignment.fasta'
download.file(url = url, destfile = alignment_file)
# run trimal with automated1 method
trimal(arglist = c('-in', alignment_file, '-out', 'trimal_results.fasta',
'-automated1', '-fasta'), outdir = wd)
# verify
list.files(wd)
#> [1] "example_alignment.fasta" "trimal_results.fasta"
readal
library(outsider)
# import
readal <- module_import('readal', repo = 'dombennett/om..trimal')
# help
readal('-h')
#>
#> readAl v1.4.rev22 build[2015-05-21]. 2009-2015. Salvador Capella-Gutierrez and Toni Gabaldón.
#>
#> readAl webpage: http://trimal.cgenomics.org
#>
#> This program is free software: you can redistribute it and/or modify
#> it under the terms of the GNU General Public License as published by
#> the Free Software Foundation, the last available version.
#>
#> Basic usage
#> readal -in <inputfile> -out <outputfile> [options].
#>
#> -h Show this information.
#> --version Show readAl version.
#>
#> -in <inputfile> Input file in several formats.
#> -out <outputfile> Output file name (default STDOUT).
#>
#> -format Print information about input file format and if sequences are aligned or not.
#> -type Print information about biological sequences datatype (e.g. nucleotides:dna, nucleotides:rna, aminoacids, etc)
#> -info Print information about sequences number, average sequence length, max & min sequence length
#>
#> -onlyseqs Generate output with only residues from input file
#>
#> -html Output residues colored according their physicochemical properties. HTML file.
#>
#> -reverse Output the reverse of sequences in input file.
#>
#> -nbrf Output file in NBRF/PIR format
#> -mega Output file in MEGA format
#> -nexus Output file in NEXUS format
#> -clustal Output file in CLUSTAL format
#>
#> -fasta Output file in FASTA format
#> -fasta_m10 Output file in FASTA format. Sequences name up to 10 characters.
#>
#> -phylip Output file in PHYLIP/PHYLIP4 format
#> -phylip_m10 Output file in PHYLIP/PHYLIP4 format. Sequences name up to 10 characters.
#> -phylip_paml Output file in PHYLIP format compatible with PAML
#> -phylip_paml_m10 Output file in PHYLIP format compatible with PAML. Sequences name up to 10 characters.
#> -phylip3.2 Output file in PHYLIP3.2 format
#> -phylip3.2_m10 Output file in PHYLIP3.2 format. Sequences name up to 10 characters.
# Real Example
# download
wd <- file.path(tempdir(), 'readal_example')
if (!dir.exists(wd)) {
dir.create(wd)
}
alignment_file <- file.path(wd, 'example_alignment.fasta')
url <- 'https://raw.githubusercontent.com/DomBennett/om..trimal/master/example_alignment.fasta'
download.file(url = url, destfile = alignment_file)
# get info
readal(arglist = c('-in', alignment_file, '-info'), outdir = wd)
#> ## Input filename 'example_alignment.fasta'
#> ## Total sequences 10
#> ## Alignment length 3161
#> ## Avg. sequence length 2943.8
#> ## Longest seq. name 'M64487_Thermococcus_celer'
#> ## Longest seq. length 3029
#> ## Shortest seq. name 'M32298_Thermoplasma_acidophilum'
#> ## Shortest seq. length 2908
# convert to phylip
readal(arglist = c('-in', alignment_file, '-out', 'example_alignment.phylip',
'-phylip_m10'), outdir = wd)
# verify
list.files(wd)
#> [1] "example_alignment.fasta" "example_alignment.phylip"
Links
Find out more by visiting the trimAL homepage.
Please cite
- trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Salvador Capella-Gutierrez; Jose M. Silla-Martinez; Toni Gabaldon. Bioinformatics 2009 25: 1972-1973.
- Bennett et al. (2020). outsider: Install and run programs, outside of R, inside of R. Journal of Open Source Software, In review
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