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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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does parsnp use -gtr from fasttree2 by default... or the fasttree2 default, which is jukes-cantor? #119

Closed Phylloxera closed 2 years ago

Phylloxera commented 2 years ago

does parsnp use -gtr from fasttree2 by default... or the fasttree2 default, which is jukes-cantor?

bkille commented 2 years ago

Parsnp runs fasttree via the following command:

fasttree -nt -quote -gamma -slow -boot 100

If you want to run fasttree with your own arguments, you can skip this step in parsnp via --skip-phylogeny step, and then use the parsnp.snps.mblocks in the output folder as input to FastTree.

Phylloxera commented 2 years ago

thanks