2025-03-14 21:59:59 -06:00
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# mashtree
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> Make a fast tree from genomes.
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> Does not make a phylogeny.
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2025-12-16 10:20:31 -07:00
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> More information: <https://github.com/lskatz/mashtree#usage>.
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2025-03-14 21:59:59 -06:00
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- Fastest method in mashtree to create a tree from fastq and/or fasta files using multiple threads, piping into a newick file:
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`mashtree --numcpus {{12}} {{*.fastq.gz}} {{*.fasta}} > {{mashtree.dnd}}`
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- Most accurate method in mashtree to create a tree from fastq and/or fasta files using multiple threads, piping into a newick file:
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`mashtree --mindepth {{0}} --numcpus {{12}} {{*.fastq.gz}} {{*.fasta}} > {{mashtree.dnd}}`
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- 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 `--`):
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`mashtree_bootstrap.pl --reps {{100}} --numcpus {{12}} {{*.fastq.gz}} -- --min-depth {{0}} > {{mashtree.bootstrap.dnd}}`
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