mashtree
Makes a fast tree from genomes.
TLDR
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]
