trimAl is a tool for the automated removal of spurious sequences or poorly aligned regions from a multiple sequence alignment. It can consider several parameters, alone or in multiple combinations, in order to select the most-reliable positions in the alignment. These include the proportion of sequences with a gap, the level of residue similarity and, if several alignments for the same set of sequences are provided, the consistency level of columns among alignments. Moreover, trimAl is able to manually select a set of columns to be removed from the alignment.
Allocate an interactive session and run the program. Sample session:
[user@biowulf]$ sinteractive -c 16 --mem 45g --gres=lscratch:20
[user@cn3144 ~]$ module load trimAl
[+] Loading singularity 3.8.5-1 on cn3144
[+] Loading trimAl 1.2rev59
[user@cn3144 ~]$ trimal
trimAl 1.2rev59. Copyright (C) 2009. 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: Salvador Capella-Gutierrez, Jose M. Silla-Martinez and
Toni Gabaldon. trimAl: a tool for automated alignment
trimming (2009).
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.
-matrix <inpufile> Input file for user-defined similarity matrix (default is Blosum62).
-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.
-clustal Output file in CLUSTAL format
-fasta Output file in FASTA format
-nbrf Output file in NBRF/PIR format
-nexus Output file in NEXUS format
-mega Output file in MEGA format
-phylip3.2 Output file in PHYLIP3.2 format
-phylip Output file in PHYLIP/PHYLIP4 format
-complementary Get the complementary alignment.
-colnumbering Get the relationship between the columns in the old and new alignment.
-select { n,l,m-k } Selection of columns to be removed from the alignment. (see User Guide).
-gt -gapthreshold <n> 1 - (fraction of sequences with a gap allowed).
-st -simthreshold <n> Minimum average similarity allowed.
-ct -conthreshold <n> Minimum consistency value allowed.
-cons <n> Minimum percentage of the positions in the original alignment to conserve.
-nogaps Remove all positions with gaps in the alignment.
-noallgaps Remove columns 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).
-resoverlap Minimum overlap of a positions with other positions in the column to be considered a "good position". (see User Guide).
-seqoverlap Minimum percentage of "good positions" that a sequence must have in order to be conserved. (see User Guide).
-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 percentage count for columns in the input alignment.
-sgt Print accumulated gap percentage count.
-scc Print conservation values for columns in the input alignment.
-sct Print accumulated conservation values count.
-sfc Print compare values for columns in the selected alignment from compare files method.
-sft Print accumulated compare values count for the selected alignment from compare files method.
-sident Print identity statistics for all sequences in the alignemnt. (see User Guide).
[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$