Science Score: 44.0%
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○Scientific vocabulary similarity
Low similarity (3.6%) to scientific vocabulary
Repository
A `snakemake` workflow for building gene trees
Basic Info
- Host: GitHub
- Owner: ryneches
- License: bsd-3-clause
- Language: Python
- Default Branch: main
- Size: 1.99 MB
Statistics
- Stars: 2
- Watchers: 3
- Forks: 0
- Open Issues: 2
- Releases: 0
Metadata Files
README.md
木槌 : kizuchi
A snakemake workflow for phylogenomic analysis of genome clusters.
kizuchi is a snakemake
workflow for building gene trees, starting from a collection of genomes
and HMM profiles, and then analyzing the phylogenetic histories of alleles
within genome-level ANI clusters. The aim of this workflow is to automate and
document gene tree analysis in a reproducible way, with the ultimate objective
of tracing recombination across timescale domains.
- gene prediction using
prodigal-gv - gene annotation using
hmmer - ortholog scoring
- amino acid alignment using
clustalo - alignment trimming using
trimal - tree inference using
fasttree - genome clustring using
fastANI - phylogenetic correlations using
SuchTree
Owner
- Name: Russell Neches
- Login: ryneches
- Kind: user
- Location: 京都府
- Company: Kyoto University
- Website: http://vort.org
- Repositories: 95
- Profile: https://github.com/ryneches
Assistant professor at Kyoto University: Evolution & ecology of viruses & microbes with a side of graph theory & machine learning. Open( Access, Science, Data )
Citation (CITATION.cff)
cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
- family-names: Neches
given-names: Russell Y.
orcid: https://orcid.org/0000-0002-2055-8381
title: "kizuchi: A snakemake workflow for phylogenomic analysis of genome clusters"
version: 1.0
doi:
date-released: 2022-06-20
GitHub Events
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Dependencies
- biopython
- cd-hit
- clustalo
- fastani
- fasttree
- hmmer
- numpy
- pandas
- pip
- polars
- prodigal-gv
- scipy
- snakemake
- trimal
- cd-hit 4.8
- clustalo 1.2.4
- fastani 1.33
- fasttree 2.1.10
- hmmer 3.2.1.*
- prodigal-gv 2.9.0-gv
- trimal 1.4