A site may have mutated on parallel lineages. Mutation can occur
on the same site across the phylogenetic lineages solved by
lineagePath. The site will be considered mutated in parallel
if the mutation occurs on the non-overlap part of more than two lineages.
The amino acid/nucleotide before and after the mutation can be allowed
different on different lineages or only the exact same mutations are
The arguments in
The minimum number of mutations to be qualified as parallel on at least two lineages. The default is 1.
The strategy for finding parallel site. The default
is to consider any mutation regardless of the amino acid/nucleotide before
and after mutation; Or
exact to force mutation to be the same; Or
post to select the site having amino acid/nucleotide