snippetbashTip
mashtree — Make a fast tree from genomes. Does not make a phylogeny. More information: <https://github.com/lska
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commandtreefromclifastmashtreegenomesmake
linux
Problem
How to use the
mashtree command: Make a fast tree from genomes. Does not make a phylogeny. More information: <https://github.com/lskatz/mashtree#usage>.Solution
mashtree — Make a fast tree from genomes. Does not make a phylogeny. More information: <https://github.com/lskatz/mashtree#usage>.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}}Code Snippets
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}}Context
tldr-pages: linux/mashtree
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