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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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parsnp v1.1 how convert XMFA to phylip/nexus/fasta ? #39

Closed Ivalize closed 6 years ago

Ivalize commented 6 years ago

Hi.

I like so much this program to explore core genome and identify SNV. But, some times i want to explort the alig (XMFA) to another format to use another program with ML method. How i can do this work? I tried with perl script but the name of strain dissapearr!, only show the index (1,2,3,4...etc).

Thanks.

Ivalize commented 6 years ago

Final answer, by me. Use a harvesttools that recognizes the aln format.

harvesttools -i parsnp.ggr -M parsnpLCB.aln