Main tool: UShER
Code repository: https://github.com/yatisht/usher
Basic information on how to use this tool:
- executable:
usher - help:
--help - version:
--version - description: UShER is a program for rapid, accurate placement of samples to existing phylogenies.
Full documentation: https://usher-wiki.readthedocs.io/en/latest/
Also contains (same version):
- matUtils
- matOptimize
- ripples
- mafft 7.526
- ucsc-fatovcf 473
- ucsc-stringify 472
# create mutation annotated tree object
usher --tree global_phylo.nh --vcf global_samples.vcf --collapse-tree --save-mutation-annotated-tree global_phylo.pb
# place samples onto tree
usher --vcf new_samples.vcf --load-mutation-annotated-tree global_phylo.pb --write-uncondensed-final-tree