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https://github.com/aaronmussig/metatree

Visualisation of polyphyletic groups between phylogenetic trees to a reference tree.

https://github.com/aaronmussig/metatree

Science Score: 23.0%

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    Found 2 DOI reference(s) in README
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    Low similarity (7.1%) to scientific vocabulary
Last synced: 9 months ago · JSON representation

Repository

Visualisation of polyphyletic groups between phylogenetic trees to a reference tree.

Basic Info
  • Host: GitHub
  • Owner: aaronmussig
  • License: gpl-3.0
  • Language: Python
  • Default Branch: master
  • Homepage:
  • Size: 177 KB
Statistics
  • Stars: 2
  • Watchers: 0
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Created almost 6 years ago · Last pushed almost 6 years ago
Metadata Files
Readme License

README.md

metatree

PyPI Conda (channel only) DOI

Visualisation of polyphyletic groups between phylogenetic trees to a given reference tree.

Installation

  • PyPI: pip install metatree
  • conda: conda install -c bioconda metatree

Usage

NOTE: The reference tree must always be the first line in the batchfile.

shell script metatree [batchfile] [out_dir] [taxonomy_file] [outgroup] [cpus]

See the example directory for an example on how to use metatree.

Changelog

0.0.1 - Initial release.

Citing

Please cite this repository if you use it in your work.

Owner

  • Name: Aaron Mussig
  • Login: aaronmussig
  • Kind: user
  • Location: Brisbane, Australia
  • Company: Australian Centre for Ecogenomics

Bioinformatics PhD student at the University of Queensland. Python and Rust enthusiast.

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Dependencies

setup.py pypi
  • biolib >=0.1.0
  • biopython *
  • dendropy >=4.1.0
  • ete3 *
  • genometreetk >0.1.2
  • matplotlib *
  • numpy *
  • pandas *
  • phylorank >0.1.0
  • scipy *
  • seaborn *
  • tqdm >=4.31.0