CmdID

CmdID / Commands

mashtree

Make a fast tree from genomes. tldr-pages

On Linux

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Linux

from tldr-pages, CC BY 4.0

Make a fast tree from genomes. Does not make a phylogeny.

Create a tree from fastq and/or fasta files using the fastest method with multiple threads, piping into a newick file

mashtree --numcpus 12 *.fastq.gz *.fasta >mashtree.dndIdentify

Create a tree from fastq and/or fasta files using the most accurate method with multiple threads, piping into a newick file

mashtree --mindepth 0 --numcpus 12 *.fastq.gz *.fasta >mashtree.dndIdentify

Create a tree with confidence values using the most accurate method (note that any options for mashtree itself have to be on the right side of the --)

mashtree_bootstrap.pl --reps 100 --numcpus 12 *.fastq.gz -- --min-depth 0 >mashtree.bootstrap.dnd