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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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Some nodes have a bootstrap value of zero; what does it mean? Can I increase number of bootstrap replicates? #131

Closed Phytobacteriology-UPNA closed 6 months ago

Phytobacteriology-UPNA commented 11 months ago

I am analyzing 59 genomes of very closely related bacteria. Probably because I'm using draft genomes, I get only a 72% of the reference covered by the alignment. Anyway, some of the branches of the resulting phylogenetic tree get a zero or 1 as bootstrap value. Can you help me with any explanation of how can this be? I uploaded a typical tree I get (in newick format)

Also, is there any way to instruct Parsnp to construct the tree using more than 100 bootstrap replicates?

Thanks for the help!

Pph_59_defC.txt

bkille commented 6 months ago

Hi @Phytobacteriology-UPNA,

Apologies for the late response. In this case, I think you are best off running Parsnp without the phylogeny step with --skip-phylogeny. Then, you can use the parsnp.snps.mblocks file in your output directory to generate the phylogeny using whichever tool/parameters you'd like.