7.5. Trimming aligned sequence data to equal length
To properly compute phylogenetic analyses on a sequence data set, the number of positions in each sequence should be equal. This includes gaps and insertions/deletions (indels) in the aligned data set, not the actual number of nucleotides or amino acids. Use your sequence alignment editor to trim the aligned files to equal size or to the size of the region you are interested in analysing (i.e. a specific domain encoded within your gene).