The c++ version can be installed manually or with conda as
conda install -c bioconda pairsnp
The c++ code can be built by running
cd ./pairsnp-cpp/
make
make install
If your compiler does not have support for open-mp you can run
make ompoff=1
The c++ version can be run from the command line as
pairsnp -c msa.fasta > output.csv
additional options include
SYNOPSIS
Fast pairwise SNP distance matrices
USAGE
pairsnp [options] alignment.fasta[.gz] > matrix.csv
OPTIONS
-h Show this help
-v Print version and exit
-s Output in sparse matrix form (i,j,distance).
-d Distance threshold for sparse output. Only distances <= d will be returned.
-k Will on return the k nearest neighbours for each sample in sparse output.
-c Output CSV instead of TSV
-i Output sequence index inplace of header (useful for downstream processing)
-t Number of threads to use (default=1)