Complementary functionality doesn't work as expected when using consistency-based methods
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scapella commented
I have detected an unexpected behaviour when trimming an alignment based on consistency methods, which compute their scores based on the level of agreement across a set of input alignment.
trimAl doesn't return those columns which are removed when applying -ct parameter. I have detected it using -ct alone or with other methods e.g. -gt
@Vicfero could you please verify to what extend this affect to the new version?