psdm: Compute a pairwise SNP distance matrix from one or two alignment(s)

Compute a pairwise SNP distance matrix from one or two alignment(s).

A key point of difference for psdm is the pairwise SNP distance between two alignment files. This is particularly beneficial if you have computed a SNP distance matrix for many samples already and want to update the distances with some new samples - without rerunning the analysis for all samples in the original file.

Another potential use is having two alignment files for the same samples but with sequences generated by different techniques. For example, if you have produced consensus sequences from SNP calls from Illumina and Nanopore and want to see how similar the Illumina-to-Nanopore (inter-technology) distances are - compared to the intra-technology distances.

Despite these motivations, psdm can still be used to compute a "traditional" pairwise SNP distance matrix for a single FASTA alignment file.

psdm is open-source and available at https://github.com/mbhall88/psdm