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.
I did a test with some Salmonella enterica genomes. When I open with Gingr the files parsnp.tree, parsnp.grr and parsnp.xmfa, the trees shown are different. Could anyone tell me what this difference in results is due to?
Hi @cfsancas, could you share some output files that we could go over. Parsnp was recently updated to include the new midpoint reroot method in dendropy. It would help us debug if needed. Thanks!
advaitb
commented
4 years ago 
cfsancas
I did a test with some Salmonella enterica genomes. When I open with Gingr the files parsnp.tree, parsnp.grr and parsnp.xmfa, the trees shown are different. Could anyone tell me what this difference in results is due to?