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splitp

Python package that implements split- and rank-based tools for inferring phylogenies, such as flattenings and subflattenings.

https://github.com/js51/splitp

Science Score: 36.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
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    Academic publication links
    Links to: zenodo.org
  • ○
    Committers with academic emails
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    Institutional organization owner
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    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (11.2%) to scientific vocabulary

Keywords

biology flattenings linear-algebra mathbio networks newick newick-format parser phylogenetics python rank split splitp subflattenings trees utas

Keywords from Contributors

mesh sequences interactive hacking
Last synced: 6 months ago · JSON representation

Repository

Python package that implements split- and rank-based tools for inferring phylogenies, such as flattenings and subflattenings.

Basic Info
Statistics
  • Stars: 1
  • Watchers: 1
  • Forks: 1
  • Open Issues: 8
  • Releases: 7
Topics
biology flattenings linear-algebra mathbio networks newick newick-format parser phylogenetics python rank split splitp subflattenings trees utas
Created over 6 years ago · Last pushed 8 months ago
Metadata Files
Readme Contributing Funding License Citation

README.md

SplitP

Coverage Status DOI

Python package which implements split- and rank-based tools for inferring phylogenies, such as flattenings and subflattenings.

Installation

The latest version of SplitP can be installed via the command pip install splitp

Example

The following computes 100 split scores from a 10000bp sequence generated from a balanced 10-taxon tree under the Jukes Cantor model.

```python

Imports

import splitp

Set parameters

sequencelength = 10000 numtaxa = 10 branchlength = 0.05 numberofsplits = 100

Define model

model = splitp.model.GTR.JukesCantor(1/2)

Generate tree, splits and alignment

tree = splitp.trees.balancednewicktree(numtaxa, branchlength) splits = splitp.allsplits(tree) alignment = splitp.generatealignment(tree, model, sequence_length)

Compute scores

for s in range(numberofsplits): split = next(splits) flattening = splitp.flattening(split, alignment, splitp.FlatFormat.reduced) score = splitp.split_score(flattening) print(split, score) ``` For more functionality please see the documentation at splitp.joshuastevenson.me.

Please see CONTRIBUTING.md for information on contributing to this project.

Owner

  • Name: Joshua Stevenson
  • Login: js51
  • Kind: user
  • Location: Australia

GitHub Events

Total
  • Create event: 1
  • Issues event: 1
  • Release event: 1
  • Issue comment event: 1
  • Push event: 4
Last Year
  • Create event: 1
  • Issues event: 1
  • Release event: 1
  • Issue comment event: 1
  • Push event: 4

Committers

Last synced: about 2 years ago

All Time
  • Total Commits: 216
  • Total Committers: 6
  • Avg Commits per committer: 36.0
  • Development Distribution Score (DDS): 0.347
Past Year
  • Commits: 12
  • Committers: 2
  • Avg Commits per committer: 6.0
  • Development Distribution Score (DDS): 0.333
Top Committers
Name Email Commits
Joshua Stevenson j****3@G****m 141
Josh j****3@g****m 68
Joshua Stevenson m****l@j****e 4
Ubuntu u****u@j****l 1
Tim Hatch t****m@t****m 1
dependabot[bot] 4****] 1
Committer Domains (Top 20 + Academic)
timhatch.com: 1 jupyter-lab-instance.novalocal: 1 joshuastevenson.me: 1

Issues and Pull Requests

Last synced: 7 months ago

All Time
  • Total issues: 13
  • Total pull requests: 24
  • Average time to close issues: 9 months
  • Average time to close pull requests: 7 days
  • Total issue authors: 1
  • Total pull request authors: 3
  • Average comments per issue: 0.08
  • Average comments per pull request: 0.17
  • Merged pull requests: 19
  • Bot issues: 0
  • Bot pull requests: 4
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • js51 (13)
Pull Request Authors
  • js51 (20)
  • dependabot[bot] (4)
  • thatch (1)
Top Labels
Issue Labels
enhancement (7) bug (1) good first issue (1) documentation (1) help wanted (1)
Pull Request Labels
dependencies (4)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 34 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 9
  • Total maintainers: 1
pypi.org: splitp

Phylogenetic tools and methods involving splits and matrix rank

  • Versions: 9
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 34 Last month
Rankings
Dependent packages count: 7.3%
Dependent repos count: 22.1%
Forks count: 22.8%
Average: 25.5%
Stargazers count: 32.0%
Downloads: 43.2%
Maintainers (1)
js51
Last synced: 6 months ago

Dependencies

requirements.txt pypi
  • networkx ==2.5
  • numpy ==1.19.5
  • pandas ==1.1.2
  • scipy ==1.5.2
.github/workflows/python-publish.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v2 composite
  • pypa/gh-action-pypi-publish 27b31702a0e7fc50959f5ad993c78deac1bdfc29 composite
.github/workflows/runpytest.yml actions
  • actions/checkout v1 composite
  • actions/setup-python v1 composite
setup.py pypi