Parsnp was designed to align the core genome of hundreds to thousands of bacterial genomes within a few minutes to few hours. Input can be both draft assemblies and finished genomes, and output includes variant (SNP) calls, core genome phylogeny and multi-alignments. Parsnp leverages contextual information provided by multi-alignments surrounding SNP sites for filtration/cleaning, in addition to existing tools for recombination detection/filtration and phylogenetic reconstruction.
Using the provided MERS and S. pneumoniae data sets parsnp fails to create a tree:
parsnp 1.2 was installed on Debian 9 using the Debian Med package . Any idea? Thanks in advance and best, Roman