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

[tallnuttrbgv]

I'm getting this error using:

trimal -in data/alignment.fasta -out outfile.fasta -ct 0.2

Why is '-in' not allowed with '-ct' ??

Using latest version compiled from source. v1.5.rev1 build[2025-11-25]

Thanks.

[nicodr97]

Hi @tallnuttrbgv,
-ct is the consistency threshold and it has to be used with -compareset. trimAl will then compare the consistency of the alignments and keep the one with the highest score. After that, it will remove any column with a consistency score below the minimum set in the -ct parameter.
So the command should be something like: trimal -compareset alignmentSet.txt -ct 0.2
Here you will find a more extended explanation https://trimal.readthedocs.io/en/latest/algorithms.html#threshold-based-trimming.
And here is the way the consistency score is calculated: https://trimal.readthedocs.io/en/latest/algorithms.html#threshold-based-trimming