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Tool for the removal of poorly aligned sequences from multiple sequence alignments. It can automatically detect and select various parameters to optimize the signal-to-noise ratio.


Sequence analysis; Sequencing; Sequence sites, features and motifs


  • Operation: Multiple sequence alignment; Sequence alignment editing
  • Input: Phylip, Fasta, Clustal, NBRF/Pir, Mega, Nexus
  • Output: Phylip, Fasta, Clustal, NBRF/Pir, Mega, Nexus, Text
  • Software interface: Command-line user interface
  • Language: C++
  • Operating system: Linux; Mac OS X; Microsoft Windows
  • License: GNU General Public License v3
  • Cost: Free
  • Version name: 1.2b - 1.4b
  • Maturity: Stable
  • Credit: FIS (06-213 to T.G.) and MEC (GEN2006-27784-E/PAT to T.G.).
  • Contact: salcagu _at_;tgabaldon _at_
  • Collection: -


Capella-Gutiérrez S, Silla-Martínez JM, Gabaldón T "trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses." Bioinformatics. 2009 Aug 1;25(15):1972-3.
PMID: 19505945
PMCID: PMC2712344

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