Hooty computes the minimum and maximum K2P distance between predetermined groups in an alignment and outputs results in a matrix format. It also includes an option for the interpretation of ambiguous bases.
Hooty takes as input a FASTA file and a text file containing a partition of species. The output is a matrix with the minimum and maximum K2P distances between the groups.
cargo install hooty
hooty <alignment.fasta> <partition.txt>
Hooty can also compute the full pairwise K2P distances between all sequences in the alignment.
hooty <alignment.fasta> <partition.txt> --full-matrix <full_matrix.csv>
You can find the complete documentation and all the available options for Hooty here.