inab/trimal

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A tool for automated alignment trimming in large-scale phylogenetic analyses. Development version: 2.0

Stars: 271
Forks: 48
Open beginner issues: 0
Indexed issues: 34

Dominant language: C++
License: GPL-3.0
Last GitHub push: Jul 14, 2026
Latest indexed: Sep 20, 2026
Contributing guide: No contributing guide
Code of conduct: No code of conduct
Beginner labels: No beginner labels indexed
PR merge metrics: No merged PRs in 30d

Beginner friendly Everything

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34 open issues indexed

-ct option ERROR: Not allowed in combination with -in option. Open

Difficulty 3/5 1-2 days Newbie friendliness 45/100

inab/trimal#128 · 1 comment · Opened May 6, 2026
-resoverlap / -seqoverlap option is extremely slow for very large alignments Open

Difficulty 4/5 3-5 days Newbie friendliness 38/100

inab/trimal#127 · 2 comments · Opened Mar 14, 2026
Update sequence coordinates after trimming gappy ends Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

inab/trimal#119 · 2 comments · Opened Oct 13, 2025
Better understand corner case for gappyout Open

inab/trimal#65 · 1 reaction · 1 assignee · Opened Apr 28, 2022
managing/ignoring warnings Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

inab/trimal#64 · Opened Apr 28, 2022
Between '-backtrans' and '-nogaps' parameter, Which one to use first? Open

Difficulty 4/5 3-5 days Newbie friendliness 20/100

inab/trimal#63 · Opened Jan 6, 2022
Option to remove all ambiguous columns Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

inab/trimal#57 · Opened Apr 22, 2020
Does trimal have a codon alignment option ? Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

inab/trimal#55 · Opened Dec 11, 2019
trimAl doesn't recognise alignment Open

Difficulty 4/5 3-5 days Newbie friendliness 28/100

inab/trimal#53 · 5 comments · Opened Jul 30, 2019
Complementary functionality doesn't work as expected when using consistency-based methods Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

inab/trimal#48 · Opened Mar 24, 2019
Removing sequences with manual overlap Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

inab/trimal#47 · 3 comments · Opened Jan 10, 2019
Redundant asignation on Sequences Matrix = operator Open

Difficulty 1/5 Under an hour Newbie friendliness 25/100

inab/trimal#46 · 1 comment · Opened Oct 16, 2018
Compareset ends without reporting when one alignment couldn't be loaded Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

inab/trimal#42 · Opened Feb 26, 2018
removing alignment length to taxon name? Open

Difficulty 3/5 1-2 days Newbie friendliness 25/100

inab/trimal#41 · 1 comment · Opened Feb 13, 2018
Improve columns mapping Open

inab/trimal#35 · 1 assignee · Opened Oct 5, 2017
readAl / trimAl creates an empty file when trying to output a non-aligned format/alignment to an aligned-format. Open

Difficulty 2/5 1-3 hours Newbie friendliness 45/100

inab/trimal#34 · 1 comment · Opened Aug 4, 2017
BLOSUM45 error Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

inab/trimal#31 · Opened May 31, 2017
duplicate sequence IDs Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

inab/trimal#30 · Opened Apr 29, 2017
Add an option for avoiding dumping any output alignment Open

inab/trimal#29 · 1 assignee · Opened Nov 17, 2016
Problem with "n" Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

inab/trimal#28 · 2 comments · 3 reactions · Opened Nov 16, 2016
Accept stdin as input Open

inab/trimal#24 · 5 comments · 1 reaction · 1 assignee · Opened Nov 8, 2015
degenerete codes in alignments Open

Difficulty 5/5 Over a week Newbie friendliness 20/100

inab/trimal#22 · Opened May 19, 2015
Any plans for multi-threading support in trimAl ? Open

inab/trimal#21 · 2 comments · 2 reactions · 1 assignee · Opened Apr 4, 2015
statal - alphabet distribution report Open

inab/trimal#20 · 2 comments · 1 assignee · Opened Apr 4, 2015
statal - basic report with #seq Open

inab/trimal#19 · 2 comments · 1 assignee · Opened Apr 4, 2015
trimAl capital letters Open

inab/trimal#13 · 1 assignee · Opened Aug 28, 2014
Implement support for different genetic codes Open

inab/trimal#12 · 1 comment · 1 assignee · Opened Aug 28, 2014
Implement Stockholm format support Open

inab/trimal#11 · 1 assignee · Opened Aug 1, 2014
Implement ATX alignments support Open

inab/trimal#10 · 1 assignee · Opened Aug 1, 2014
Removing sequences with a % gaps equal or greater than a threshold Open

inab/trimal#9 · 1 assignee · Opened May 23, 2014
Improving warning when working with backtranslation Open

inab/trimal#8 · 1 assignee · Opened Apr 19, 2014
Improving alignment stats Open

inab/trimal#7 · 1 assignee · Opened Jan 27, 2014
trimal changes fasta headers when contain ':' Open

inab/trimal#5 · 1 comment · 1 assignee · Opened Dec 18, 2012
Remove "{" and "}" symbols Open

inab/trimal#4 · 1 assignee · Opened Sep 5, 2011

inab/trimal

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