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marbl / parsnp

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.
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Option to skip tree building #107

Closed hkaspersen closed 2 years ago

hkaspersen commented 2 years ago

Hello, and thank you for a great tool!

I am using ParSNP mostly for alignments, so I was wondering if it was possible to perhaps add an option that skips the tree reconstruction? It adds a lot to the runtime of the tool for me.

Thanks in advance!

bkille commented 2 years ago

Hi @hkaspersen! The recently added --skip-phylogeny argument in v1.6.1 should do exactly this for you.

hkaspersen commented 2 years ago

Thank you forthe swift reply! I will check out that option.