recipe phame

A tool to derive SNP matrices and phylogenetic tree from raw reads, contigs, and full genomes.

Homepage

https://github.com/LANL-Bioinformatics/PhaME

License

GPLV2

Recipe

/phame/meta.yaml

Links

biotools: phame

package phame

(downloads) docker_phame

Versions

1.0.3-0, 1.0.2-0, 1.0.1-0, 1.0.0-1, 1.0-0

Depends bbmap

>=37.62

Depends bcftools

>=1.7

Depends bowtie2

>=2.3.4.1

Depends bwa

>=0.7.12

Depends cmake

>=3.0.1

Depends curl

>=7.60.0

Depends fasttree

>=2.1.9

Depends hyphy

>=2.3.12

Depends iqtree

>=1.6.7

Depends mafft

>=7.313

Depends mummer

>=3.23

Depends muscle

>=3.8.31

Depends openmpi

>=3.1.0

Depends paml

>=4.9

Depends perl

Depends perl-app-cpanminus

>=1.7039

Depends perl-bioperl

>=1.7.2

Depends perl-file-path

>=2.12

Depends perl-getopt-long

>=2.50

Depends perl-io-handle

>=1.28

Depends perl-io-handle

>=1.35

Depends perl-parallel-forkmanager

>=1.17

Depends perl-statistics-distributions

>=1.02

Depends raxml

>=8.2.10

Depends samtools

>=1.7

Requirements

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install phame

and update with:

conda update phame

or use the docker container:

docker pull quay.io/biocontainers/phame:<tag>

(see phame/tags for valid values for <tag>)