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Open Source Science

https://github.com/compevol/beast2

Bayesian Evolutionary Analysis by Sampling Trees

https://github.com/compevol/beast2

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
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    8 of 61 committers (13.1%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (13.7%) to scientific vocabulary

Keywords

bayesian-inference beast evolution java mcmc phylogenetics

Keywords from Contributors

linguistics cross-linguistic-data concepts bioinformatics sequencing phylogenetic-trees genomics ngs usegalaxy workflow-engine
Last synced: 5 months ago · JSON representation

Repository

Bayesian Evolutionary Analysis by Sampling Trees

Basic Info
  • Host: GitHub
  • Owner: CompEvol
  • License: lgpl-2.1
  • Language: Java
  • Default Branch: master
  • Homepage: www.beast2.org
  • Size: 93.8 MB
Statistics
  • Stars: 255
  • Watchers: 39
  • Forks: 85
  • Open Issues: 193
  • Releases: 41
Topics
bayesian-inference beast evolution java mcmc phylogenetics
Created about 12 years ago · Last pushed 6 months ago
Metadata Files
Readme License

README.md

BEAST 2

Build Status

BEAST is a cross-platform program for Bayesian inference using MCMC of molecular sequences. It is entirely oriented towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability. We include a simple to use user-interface program for setting up standard analyses and a suit of programs for analysing the results.

NOTE: This directory contains the BEAST 2 source code, and is therefore of interest primarily to BEAST 2 developers. For binary releases, user tutorials and other information you should visit the project website at beast2.org.

Development Rules and Philosophy

Aspects relating to BEAST 2 development such as coding style, version numbering and design philosophy are discussed on the BEAST 2 web page at beast2.org/package-development-guide/core-development-rules.

License

BEAST 2 is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. A copy of the license is contained in the file COPYING, located in the root directory of this repository.

This software is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License contained in the file COPYING for more details.

Owner

  • Name: Computational Evolution Group
  • Login: CompEvol
  • Kind: organization
  • Location: University of Auckland, Auckland, New Zealand

GitHub Events

Total
  • Create event: 2
  • Release event: 1
  • Issues event: 48
  • Watch event: 20
  • Issue comment event: 71
  • Push event: 40
  • Pull request event: 2
  • Fork event: 3
Last Year
  • Create event: 2
  • Release event: 1
  • Issues event: 48
  • Watch event: 20
  • Issue comment event: 71
  • Push event: 40
  • Pull request event: 2
  • Fork event: 3

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 2,834
  • Total Committers: 61
  • Avg Commits per committer: 46.459
  • Development Distribution Score (DDS): 0.418
Past Year
  • Commits: 70
  • Committers: 12
  • Avg Commits per committer: 5.833
  • Development Distribution Score (DDS): 0.4
Top Committers
Name Email Commits
Remco Bouckaert h****l@g****m 1,649
Tim Vaughan t****n@g****m 280
Alexei Drummond a****d@g****m 207
walterxie d****e@g****m 157
Joseph Heled j****d@g****m 118
Walter w****e 82
Andrew Rambaut a****t@e****k 49
Denise Kühnert d****t@g****m 23
Tim Vaughan t****v@u****z 22
Alex Popinga a****a@g****m 17
Jessie Wu a****s@g****m 17
Sasha s****a@a****z 16
jordandouglas j****s@w****m 15
Gereon Kaiping a****y@y****e 15
Sasha g****a@g****m 13
walterxie w****r@c****z 12
kche309 8****9 11
1j h****n@s****k 10
rbouckaert h****l@g****m 10
Simon J Greenhill S****l 8
Alex Popinga a****a@g****m 8
Arman Bilge a****e@g****m 8
Remco Bouckaert r****o@R****l 7
rbou019 r****9@c****z 7
Benjamin Redelings b****s@g****m 6
Luke Maurits l****e@m****u 5
Huw A. Ogilvie h****e@a****u 5
Alexander Alekseyenko a****o@g****m 4
cinthylorein b****y@g****m 3
Wytamma Wirth w****h@m****m 3
and 31 more...
Committer Domains (Top 20 + Academic)
cs.auckland.ac.nz: 2 ed.ac.uk: 1 ughan.xyz: 1 auckland.ac.nz: 1 windowslive.com: 1 yahoo.de: 1 stats.ox.ac.uk: 1 googl.com: 1 cs-294937.sfac.auckland.ac.nz: 1 maurits.id.au: 1 anu.edu.au: 1 me.com: 1 hum.leidenuniv.nl: 1 gmial.com: 1 uoa.auckland.ac.nz: 1 aucklanduni.ac.nz: 1 ucla.edu: 1 geo.uzh.ch: 1 wifi-guest-172-24-109-97.net.auckland.ac.nz: 1 wifi-guest-172-24-82-230.net.auckland.ac.nz: 1 rc.ufl.edu: 1 id.ethz.ch: 1 env.ethz.ch: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 23
  • Total pull requests: 2
  • Average time to close issues: 3 days
  • Average time to close pull requests: about 8 hours
  • Total issue authors: 15
  • Total pull request authors: 2
  • Average comments per issue: 1.22
  • Average comments per pull request: 0.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 23
  • Pull requests: 2
  • Average time to close issues: 3 days
  • Average time to close pull requests: about 8 hours
  • Issue authors: 15
  • Pull request authors: 2
  • Average comments per issue: 1.22
  • Average comments per pull request: 0.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • rbouckaert (12)
  • walterxie (7)
  • jordandouglas (4)
  • alexeid (3)
  • jacklo225 (2)
  • jjmccollum (2)
  • Chonghao98 (2)
  • ViralVerity (1)
  • dmsoong (1)
  • SimonGreenhill (1)
  • m-d-grunnill (1)
  • hrzolix (1)
  • jugne (1)
  • CiaccioE (1)
  • asad-869 (1)
Pull Request Authors
  • jordandouglas (1)
  • tgvaughan (1)
  • EvaLiyt (1)
  • rbouckaert (1)
  • walterxie (1)
Top Labels
Issue Labels
defect (6) enhancement (3) BEAUti (2) documentation (1) code style (1)
Pull Request Labels

Packages

  • Total packages: 2
  • Total downloads: unknown
  • Total dependent packages: 0
    (may contain duplicates)
  • Total dependent repositories: 0
    (may contain duplicates)
  • Total versions: 80
proxy.golang.org: github.com/CompEvol/beast2
  • Versions: 40
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent packages count: 5.3%
Average: 5.5%
Dependent repos count: 5.7%
Last synced: 6 months ago
proxy.golang.org: github.com/compevol/beast2
  • Versions: 40
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent packages count: 5.3%
Average: 5.5%
Dependent repos count: 5.7%
Last synced: 6 months ago

Dependencies

.github/workflows/beauti.yml actions
  • actions/checkout v2 composite
.github/workflows/core.yml actions
  • actions/checkout v2 composite
Dockerfile docker
  • openjdk 11 build