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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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How many bootstrap replicates are made for tree reconstruction with Parsnp? #67

Closed Phytobacteriology-UPNA closed 4 years ago

Phytobacteriology-UPNA commented 4 years ago

Hi! Thanks a lot for this wonderful software, which made my research so much easier! I made a SNPs tree using Parsnp for a collection of bacteria, and I got a newick tree that was imported to Mega7 for manipulation. The tree comes with bootstrap support. We are in the process of publishing, and we were wondering how many bootstrap replicates are made by Parsnp. We could not find any way to control this parameter (not that it matters), nor information on the actual number. I would greatly appreciate if you could let me know how many replicates are made. Thanks very much!

advaitb commented 4 years ago

Hi @Phytobacteriology-UPNA,

Parsnp uses Fastree for ML-tree generation and uses and runs it with a bootstrap value (-boot) of 100.