AB Enforce Triplets

--enforce_triplets, -et

Description

Reorder gaps in a pre-existing nucleotide alignment to create triplets. Each sequence is considered independently of the others, and residues/gaps are moved the minimum distance necessary to fulfill each triplet.

Note that this is not the same as performing a protein alignment and mapping back to nucleotides. In most cases the actual alignment score will be worse following this transformation, although, due to purifying selection against frame-shift mutations in coding sequences, the new alignment may be preferable from an evolutionary perspective.

Example

Input file: Mle-Panx_C-term.phy

 5 62
Mle-Panxα9   atgt------tagacatactttca-aagtttaaaggagt-tactcctttt----aaaggtat
Mle-Panxα7A  atggggg-tggaaattctgtttcc-cataatcaacagagccaccgctccgatc--aagtctg
Mle-Panxα1   atgtactggatatttgagatttgt-caagagataaagcgagctcaatcctgccgaaagttcg
Mle-Panxα3   atgt---tgttgctcggctcactcggaacgatc-aagaacttgagcatcttc--aaagacct
Mle-Panxα12  atg------gttattgacatcctctccggtttt-aaggggatcacgcccttc--aaaggcat

Usage example

$: alb Mle-Panx_C-term.phy -et

Output

 5 62
Mle-Panxα9   atgtta------gacatactttca---aagtttaaaggagttactcctttt---aaaggtat
Mle-Panxα7A  atgggggtg---gaaattctgtttcccataatcaacagagccaccgctccgatcaagtctg-
Mle-Panxα1   atgtactggatatttgagatttgtcaagagataaagcgagctcaatcctgccgaaagttcg-
Mle-Panxα3   atgttg---ttgctcggctcactcggaacgatc---aagaacttgagcatcttcaaagacct
Mle-Panxα12  atg------gttattgacatcctctccggtttt---aaggggatcacgcccttcaaaggcat