trimAl v1.1 command line version manual

Input and Output formats

trimAl reads and produce multiple sequence alignments in Phylip interleaved format

Basic usage

  trimal -in <inputfile> -out <outputfile> -(other options) 

Common options

  • -in <inputfile> Input file in PHYLIP format
  • -out <outputfile> Output alignment in PHYLIP format (default stdout)
  • -matrix <inpufile> Input file for user-defined similarity matrix (default is Blosum62)
  • -compareset <inputfile> Input list of paths for the files containing the alignments to compare
  • -gt -gapthreshold <n> (1 - n) maximum gap percentage allowed
  • -st -simthreshold <n> Minimum average similarity allowed
  • -ct -comthreshold <n> Minimum comparison value allowed
  • -cons -conserve <n> Minimum percentage of the positions in the original alignment to conserve (overrides any threshold)
  • -w <n> (half)window size, score of position i is the average of the window (i - n) to (i + n)
  • -nogaps Remove all positions with gaps in the alignment (equivalent to -gt 0 -conserve 0)
  • -strict Use automatic selection on “strict” mode(see User Guide)
  • -relaxed Use automatic selection on “relaxed” mode(see User Guide)
  • -sgc Print gap percentage count for columns in the input alignment
  • -sct Print accumulated gap percentage count
  • -sgt Print conservation values for comlumns in the input alignment


1) Removes all positions in the alignment with gaps in 10% or more of the sequences, unless this leaves less than 60%. In such case, print the 60% best (with less gaps) positions.

      trimal -in <inputfile> -out <outputfile> -gt 10 -cons 60 

2) As above but, the gap percentage is averaged over a window starting 3 positions before and ending 3 positions after the column.

trimal -in <inputfile> -out <outputfile> -gt 10 -cons 60 -w 3

3) Uses an automatic (strict) heuristic to decide optimal thresholds, based in the gap percentage count over the whole alignment. (see User Guide for details)

      trimal -in <inputfile> -out <outputfile> -extrict

Use of a user defined similarity-matrix

To compute a similarity score for protein alignments, trimAl uses the Blosum62 amino acid similarity matrix by default. However, the user can upload any other matrix.

Allowed combinations

The next image shows all the possible combinations of trimAl's options.

trimal1.1/trimal_v1.1_command_line_version_manual.txt · Last modified: 2009/04/19 18:17 by scapella
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