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https://github.com/4ment/physher

A multi-algorithmic framework for phylogenetic inference

https://github.com/4ment/physher

Science Score: 39.0%

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  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
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    .zenodo.json file
    Found .zenodo.json file
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    DOI references
    Found 12 DOI reference(s) in README
  • ○
    Academic publication links
  • ○
    Committers with academic emails
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    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (12.8%) to scientific vocabulary

Keywords

bayesian-inference c genetic-algorithm maximum-likelihood mcmc phylogenetics variational-inference
Last synced: 5 months ago · JSON representation

Repository

A multi-algorithmic framework for phylogenetic inference

Basic Info
  • Host: GitHub
  • Owner: 4ment
  • License: gpl-2.0
  • Language: C
  • Default Branch: master
  • Homepage:
  • Size: 2.5 MB
Statistics
  • Stars: 14
  • Watchers: 6
  • Forks: 2
  • Open Issues: 2
  • Releases: 6
Topics
bayesian-inference c genetic-algorithm maximum-likelihood mcmc phylogenetics variational-inference
Created almost 11 years ago · Last pushed 8 months ago
Metadata Files
Readme License

README.md

physher

CMake License: GPL v2

About physher

physher is a program for estimating evolutionary rates and divergence times from genetic, amino acid, codon, and generic data.

The current version of physher is incompatible with the first version. Documentation for installing physher1 can be found here and the manual is located here.

Getting Started

A C compiler such as gcc or clang is required. It is also requires the GSL library. On Debian-based systems, dependencies can be installed via apt:

bash sudo apt install gcc gsl

On MacOS, dependencies can be installed using a package manager such as Homebrew. bash brew install llvm gsl

Other package managers such as conda and MacPorts can also be used to install dependencies.

Dependencies

Installation

To build physher from source you can run bash git clone https://github.com/4ment/physher cmake -S physher/ -B physher/build cmake --build physher/build/ --target install

Check install

If the installation was successful, this command should print the version of physher bash physher

Building C++ wrappers (optional)

A subset of physher's functionalities is exposed in C++ wrappers. These wrappers are used in torchtree, a python program, through bindings and torchtree-physher. A C++ compiler such as g++ or clang++ is required. Compilers can be installed using apt or homebrew

bash git clone https://github.com/4ment/physher cmake -S physher/ -B physher/build -DBUILD_CPP_WRAPPER=on cmake --build physher/build/ --target install

Testing (optional)

bash cmake -S physher/ -B physher/build -DBUILD_TESTING=on cmake --build physher/build/ --target install ctest --test-dir physher/build/

Quick start

bash cd examples/fluA physher JC69-time-ELBO.json

physher in action

Some examples of projects using physher - marginal-experiments: Evaluation of 19 dubious ways to compute marginal likelihood estimates. 10.1093/sysbio/syz046. - phylostan: Comparison of phylostan and physher using variational inference. 10.1101/702944. - gradient-benchmark: Benchmarking of automatic differentiation and analical gradients. 10.1093/gbe/evad099 - torchtree-physher: Plugin provinding fast calculation of phylogenetic functions in physher to torchtree.

License

Distributed under the GPLv2 License. See LICENSE for more information.

Citing physher

Fourment M and Holmes EC. Novel non-parametric models to estimate evolutionary rates and divergence times from heterochronous sequence data. BMC Evolutionary Biology, 2014. doi: 10.1186/s12862-014-0163-6

Owner

  • Name: Mathieu Fourment
  • Login: 4ment
  • Kind: user
  • Location: Australia
  • Company: University of Technology Sydney

GitHub Events

Total
  • Issues event: 2
  • Push event: 2
  • Fork event: 1
  • Create event: 3
Last Year
  • Issues event: 2
  • Push event: 2
  • Fork event: 1
  • Create event: 3

Committers

Last synced: 10 months ago

All Time
  • Total Commits: 417
  • Total Committers: 2
  • Avg Commits per committer: 208.5
  • Development Distribution Score (DDS): 0.002
Past Year
  • Commits: 2
  • Committers: 1
  • Avg Commits per committer: 2.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Mathieu Fourment m****t@g****m 416
Google Code Exporter G****r 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 2
  • Total pull requests: 0
  • Average time to close issues: 6 months
  • Average time to close pull requests: N/A
  • Total issue authors: 2
  • Total pull request authors: 0
  • Average comments per issue: 0.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
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
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Top Authors
Issue Authors
  • jessiepelosi (1)
  • UdayanJ (1)
  • benjamin-lieser (1)
Pull Request Authors
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