Supermatrix alignment length is not a multiple of 3!
Hi! I've finished agalma phylogenetics pipeline exactly as described in the tutorial on 4 real transcriptomes.
The lengths of resulting nucleotide supermatrix alignment is not a multiple of 3! When looking in gblocks-nuc folder, which contains per gene alignments, I see 1722 alignments and 1132 out of these 1722 have not 3x lengths.
What should I do to check these alignments? If alignment length is not 3x, it might be that somewhere are problems with reading frame, so I cant trust the aa-alignment.
Is this a problem of gblocks or macse?