0.6.3

UShER container

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

Additional dependencies

• mafft 7.526
• ucsc-fatovcf 473
• ucsc-stringify 472

Example Usage

# 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