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.
How can I determine which FastTree, MUSCLE and PhiPack options were used when I run parsnp? I'm particularly interested in knowing which model of nucleotide evolution is used and what the unit of scale is in the output tree. I didn't see anything useful in the parsnpAligner.log or .ini files.
gotero
commented
8 years ago
How can I determine which FastTree, MUSCLE and PhiPack options were used when I run parsnp? I'm particularly interested in knowing which model of nucleotide evolution is used and what the unit of scale is in the output tree. I didn't see anything useful in the parsnpAligner.log or .ini files.
Thanks!
Glen