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inab / trimal

A tool for automated alignment trimming in large-scale phylogenetic analyses. Development version: 2.0
https://trimal.readthedocs.io/
GNU General Public License v3.0
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WARNING: Removing column '743' composed only by gaps #71

Closed MaxBai0123 closed 9 months ago

MaxBai0123 commented 1 year ago

image Hi~,I used trimal to trim my mafft result, but it tell me warning, I not't know why？

NickSomsen commented 1 year ago

It probably means that the automated filtering resulted in columns 743 and 1697 to be completely composed out of gaps, i.e. every single sequence has a gap in the alignment at those 2 positions. These gap columns can then be removed since they do not give any information anymore. (this is the result of the -noallgaps option which seems to be used automatically when using automated1).

The same can happen with entire sequences, it will then give a warning like the following:

WARNING: Removing sequence '>my_seq' composed only by gaps

This can however be prevented by using the -keepseqs option.