mashtree

Make 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