tldr/pages/linux/mashtree.md

mashtree

Makes a fast tree from genomes. Does not make a phylogeny. More information: https://github.com/lskatz/mashtree.

• Fastest method in mashtree to create a tree from fastq and/or fasta files using multiple threads, piping into a newick file:

mashtree --numcpus {{12}} {{*.fastq.gz}} {{*.fasta}} > {{mashtree.dnd}}

• Most accurate method in mashtree to create a tree from fastq and/or fasta files using multiple threads, piping into a newick file:

mashtree --mindepth {{0}} --numcpus {{12}} {{*.fastq.gz}} {{*.fasta}} > {{mashtree.dnd}}

• Most accurate method to create a tree with confidence values (note that any options for mashtree itself has to be on the right side of the --):

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