# Pair selection must retain codons at tree positions 4 and 8 in each chain.
# Reversible model tests do not cover log pairing; retain with native sample selection.
template.fasta -A samples.fastas -T samples.trees -A samples.fastas -T samples.trees -n query.tree --alphabet Codons(DNA,standard) --subsample=2 --skip=3 --until=8 --thin=2

