Phylogemetric
Phylogemetric: A Python library for calculating phylogenetic network metrics - Published in JOSS (2016)
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Published in Journal of Open Source Software
Keywords
Repository
Python library for calculating the delta score (Holland et al. 2002) and Q-Residual (Gray et al. 2010)
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README.md
phylogemetric
A python library for calculating delta score (Holland et al. 2002) and Q-Residual (Gray et al. 2010) for phylogenetic data.
Installation:
Installation is only a pip install away:
shell
pip install phylogemetric
Usage: Command line
Basic usage:
```shell
phylogemetric
usage: phylogemetric [-h] method filename ```
Calculate delta score for filename example.nex:
```shell
phylogemetric delta example.nex
taxon1 0.2453 taxon2 0.2404 taxon3 0.2954 ... ```
Calculate qresidual score for filename example.nex:
```shell
phylogemetric qresidual example.nex
taxon1 0.0030 taxon2 0.0037 taxon3 0.0063 ... ```
Note: to save the results to a file use shell piping e.g.:
```shell
phylogemetric qresidual example.nex > qresidual.txt ```
Speeding things up by using multiple processes.
You can tell phylogemetric to use multiple cores with the -w/--workers argument:
```shell
phylogemetric -w 4 qresidual example.nex ```
Usage: Library
Calculate scores:
```python from nexus import NexusReader from phylogemetric import DeltaScoreMetric from phylogemetric import QResidualMetric
load data from a nexus file:
nex = NexusReader("filename.nex") qres = QResidualMetric(nex.data.matrix)
Or construct a data matrix directly:
matrix = { 'A': [ '1', '1', '1', '1', '0', '0', '1', '1', '1', '0', '1', '1', '1', '1', '0', '0', '1', '1', '1', '0' ], 'B': [ '1', '1', '1', '1', '0', '0', '0', '1', '1', '1', '1', '1', '1', '1', '1', '0', '0', '1', '1', '1' ], 'C': [ '1', '1', '1', '1', '1', '1', '1', '0', '1', '1', '1', '0', '0', '0', '0', '1', '0', '1', '1', '1' ], 'D': [ '1', '0', '0', '0', '0', '1', '0', '1', '1', '1', '1', '0', '0', '0', '0', '1', '0', '1', '1', '1' ], 'E': [ '1', '0', '0', '0', '0', '1', '0', '1', '0', '1', '1', '0', '0', '0', '0', '1', '1', '1', '1', '1' ], }
delta = DeltaScoreMetric(matrix) ```
Class Methods:
```python
m = DeltaScoreMetric(matrix)
calculates the number of quartets in the data:
m.nquartets()
returns the distance between two sequences:
m.dist(['1', '1', '0'], ['0', '1', '0'])
gets a dictionary of metric scores:
m.score() m.score(workers=4) # with multiple processes.
pretty prints the metric scores:
m.pprint()
```
Requirements:
- python-nexus >= 1.1
Performance Notes:
Currently phylogemetric is implemented in python, and the Delta/Q-Residual algorithms are O(n). This means
that performance is not optimal, and it may take a while to calculate these metrics for datasets with more than
100 taxa or so. To help speed this up, use the multiple processes argument -w/--workers at the command line or by passing workers=n to the score function.
I hope to improve performance in the near future, but in the meantime, if this is an issue for you then try using the implementations available in SplitsTree.
Citation:
If you use phylogemetric, please cite:
Greenhill, SJ. 2016. Phylogemetric: A Python library for calculating phylogenetic network metrics. Journal of Open Source Software.
http://dx.doi.org/10.21105/joss.00028
Changelog:
- 1.2.2: performance improvements
- 1.2.1: bug fix
- 1.2.0: performance improvements
- 1.1.0:
- Added support for multiple processes.
- Removed python 2 support.
Acknowledgements:
- Thanks to David Bryant for clarifying the Q-Residual code.
- Thanks to Kristian Rother for code quality suggestions.
Owner
- Name: Simon J Greenhill
- Login: SimonGreenhill
- Kind: user
- Location: Jena, Canberra, Auckland
- Company: @shh-dlce @eva-dlce
- Website: http://simon.net.nz
- Twitter: SimonGreenhill
- Repositories: 11
- Profile: https://github.com/SimonGreenhill
I study how languages and cultures evolve. Scientist at the University of Auckland, and the Max Planck Institute for Evolutionary Anthropology
JOSS Publication
Phylogemetric: A Python library for calculating phylogenetic network metrics
Authors
ARC Centre of Excellence for the Dynamics of Language, Australian National University
Editor
Arfon Smith
Tags
phylogenetic language evolution cultural evolution network metricsCodeMeta (codemeta.json)
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"@id": "http://orcid.org/0000-0001-7832-6156",
"@type": "Person",
"email": "simon@simon.net.nz",
"name": "Simon J. Greenhill",
"affiliation": "ARC Centre of Excellence for the Dynamics of Language, Australian National University"
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"identifier": "http://dx.doi.org/10.5281/zenodo.55663",
"codeRepository": "https://github.com/SimonGreenhill/phylogemetric",
"datePublished": "2016-06-15",
"dateModified": "2016-06-15",
"dateCreated": "2016-06-15",
"description": "A Python library for calculating the delta score (Holland et al. 2002) and Q-Residual (Gray et al. 2010)",
"keywords": "phylogenetic, language evolution, cultural evolution, network metrics",
"license": "BSD",
"title": "phylogemetric",
"version": "v1.0.0"
}GitHub Events
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| Name | Commits | |
|---|---|---|
| SimonGreenhill | s****n@s****z | 106 |
| Kristian Rother | k****r@r****e | 1 |
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pypi.org: phylogemetric
A python library for calculating the delta score (Holland et al. 2002) and Q-Residual (Gray et al. 2010)
- Homepage: https://github.com/SimonGreenhill/phylogemetric
- Documentation: https://phylogemetric.readthedocs.io/
- License: BSD
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Latest release: 1.2.2
published almost 4 years ago
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Dependencies
- python-nexus >=1.1
- pythran >=0.10.0
- numpy *
- python-nexus *
- pythran *