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

Status: Open.

#128 In inab/trimal;

· tallnuttrbgv opened on May 6, 2026

-resoverlap / -seqoverlap option is extremely slow for very large alignments

Status: Open.

#127 In inab/trimal;

· Mvila035 opened on Mar 14, 2026

Update sequence coordinates after trimming gappy ends

Status: Open.

#119 In inab/trimal;

· vagkaratzas opened on Oct 13, 2025

Better understand corner case for gappyout

Status: Open.

#65 In inab/trimal;

· scapella opened on Apr 28, 2022

managing/ignoring warnings

Status: Open.

#64 In inab/trimal;

· scapella opened on Apr 28, 2022

Between '-backtrans' and '-nogaps' parameter, Which one to use first?

Status: Open.

#63 In inab/trimal;

· kishor2019 opened on Jan 6, 2022

Option to remove all ambiguous columns

Status: Open.

#57 In inab/trimal;

· vatanparast opened on Apr 22, 2020

Does trimal have a codon alignment option ?

Status: Open.

#55 In inab/trimal;

· BenjaminGuinet opened on Dec 11, 2019

trimAl doesn't recognise alignment

Status: Open.

#53 In inab/trimal;

· honeyella opened on Jul 30, 2019

Complementary functionality doesn't work as expected when using consistency-based methods

Status: Open.

#48 In inab/trimal;

· scapella opened on Mar 24, 2019

Removing sequences with manual overlap

Status: Open.

#47 In inab/trimal;

· bruceamurphy opened on Jan 10, 2019

Redundant asignation on Sequences Matrix = operator

Status: Open.

#46 In inab/trimal;

· Vicfero opened on Oct 16, 2018

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