I cannot find documentation on how much data cleandata = 1 removes in codeml. For example, if there are 40 sequences in an alignment and in one column only 1 sequence has an ambiguity or a gap character, is that whole column still removed? Is there a way to set a buffer for how much can be removed? Like if only 10% of the sequences have a gap, then it is okay to keep those gaps to avoid losing information for all the other sequences?
Is this possible, or if there are any gaps/ambiguities anywhere that whole column is gone?