pkg/

Package alphabet provides mappings between codons and amino acids

Package closest provides routines to find the closest sequences to a set of query sequences, by genetic distance

Package encoding provides mappings between character representations of nucleotides and bitwise encodings, for fast sequence comparison.

Package fastaio provides functions for reading and writing fasta format files

TO DO

Package gfio provides io functionality, including to/from stdin/stderr, and helpful error messages when used in combination with bad filepaths from commandline options

Package sam provides functionality to handle sam format files.

Package snps implements functions to call nucleotide changes between each sequence in a fasta format alignment and a reference sequence.

Package updown implements functions that calculate pseudo-tree aware snp-distances between sequences.

Package variants implements functionality to annotate mutations relative to a reference sequence for all records in a multiple sequence alignment in fasta format.