trimal

TAFFISH wrapper for trimAl 1.5.1, a command-line suite for automated trimming, conversion, and summary statistics of multiple sequence alignments used in phylogenetic analyses.

Package identity:

• App: trimal
• Command: taf-trimal
• Kind: tool
• TAFFISH release: 1.5.1-r1
• Container image: ghcr.io/taffish/trimal:1.5.1-r1
• Upstream: inab/trimal tag v1.5.1
• Runtime version banner: trimAl/readAl/statAl v1.5.rev1 build[2025-11-25]
• Native platforms: linux/amd64, linux/arm64

Usage

Show TAFFISH wrapper help:

taf-trimal --help

Show upstream trimAl help or version:

taf-trimal -- -h
taf-trimal -- --version

Trim an alignment with the automatic heuristic:

taf-trimal \
  -in alignment.fasta \
  -out alignment.trimmed.fasta \
  -automated1

Use gap-based trimming and write an HTML summary:

taf-trimal \
  -in alignment.fasta \
  -out alignment.gappyout.fasta \
  -gappyout \
  -htmlout alignment.gappyout.html

Convert an alignment with readal:

taf-trimal readal \
  -in alignment.fasta \
  -out alignment.phy \
  -phylip

Compute alignment statistics with statal:

taf-trimal statal \
  -in alignment.fasta \
  -sgt \
  > gap-score-distribution.tsv

Back-translate a trimmed amino-acid alignment to coding DNA:

taf-trimal \
  -in protein_alignment.fasta \
  -backtrans cds_sequences.fasta \
  -out cds_alignment.trimmed.fasta \
  -automated1

Packaged Commands

The image builds the upstream v1.5.1 source release and installs:

• trimal: default command for trimming multiple sequence alignments.
• readal: alignment format conversion and inspection helper.
• statal: alignment statistics helper built by upstream make.

TAFFISH command mode is enabled, so helper commands are called as taf-trimal readal ... or taf-trimal statal .... For upstream trimAl options beginning with -, pass them directly to taf-trimal or use taf-trimal -- ... when you need to avoid wrapper option parsing.

The upstream repository also contains research/maintenance Python scripts under scripts/. This app does not expose those scripts as supported runtime commands because they are not installed by the upstream Makefile and several require extra Python/Biopython/NumPy or Python 2 compatibility. The packaged command surface is the compiled trimal, readal, and statal suite.

Inputs and Outputs

trimal accepts common MSA formats including FASTA, CLUSTAL, NEXUS, PHYLIP, and NBRF/PIR. It can write trimmed alignments to stdout or -out, generate HTML reports with -htmlout, produce column-number mapping with -colnumbering, compare sets of alignments with -compareset, and back-translate protein alignments with -backtrans.

Common trimming modes include:

• -automated1
• -gappyout
• -strict
• -strictplus
• -nogaps
• -noallgaps
• manual thresholds such as -gt, -st, -ct, and -cons
• manual column or sequence removal with -selectcols and -selectseqs

The image keeps the upstream example dataset and documentation under:

/opt/trimal/share/doc/trimal/

Platform

This app is built from source on Debian 12 and declares native linux/amd64 and linux/arm64 container builds. It does not require network access at runtime and does not download databases or models.

Boundaries

This is a tool app, not a TAFFISH flow. It exposes the upstream compiled command suite and does not run alignment generation, phylogenetic tree inference, model selection, or downstream visualization outside trimAl's own -htmlout report.

Smoke tests check version banners, help surfaces, dynamic-library linkage, automated and gap-based trimming, HTML report creation, readal conversion, statal statistics, and back-translation using upstream example data. They do not validate all possible parameter combinations or scientific suitability of a trimming strategy for a particular study.

Metadata

• Upstream repository: https://github.com/inab/trimal
• Upstream documentation: https://trimal.readthedocs.io
• Upstream release: https://github.com/inab/trimal/releases/tag/v1.5.1
• Upstream license: GPL-3.0-or-later
• Citation: Capella-Gutierrez S, Silla-Martinez JM, Gabaldon T. 2009. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses.
• DOI: 10.1093/bioinformatics/btp348
• PMID: 19505945