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Applications

Experiments

Open Sustainable Technology

https://github.com/jlsteenwyk/orthosnap

a tree splitting and pruning algorithm for retrieving single-copy orthologs from gene family trees
bioinformatics evolution evolutionary-biology genomics orthology orthology-assignments orthology-inference phylogenetics phylogenomics python
Added: over 1 year ago - Last Synced: about 1 year ago - Created: February 28, 2021

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: Python
  • Commits: 108
  • Committers: 2
  • Issues: 8
  • Pull Requests: 4
  • Owner: JLSteenwyk
  • Stars: 19
  • Forks: 1
  • Packages: 1
  • Downloads: 81
https://github.com/evogytis/baltic

baltic - backronymed adaptable lightweight tree import code for molecular phylogeny manipulation, analysis and visualisation. Development is back on the evogytis/baltic branch (i.e. here).
phylogenetics visualisation
Added: over 1 year ago - Last Synced: about 1 year ago - Created: April 22, 2016

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: Python
  • Commits: 122
  • Committers: 8
  • Issues: 25
  • Pull Requests: 10
  • Owner: evogytis
  • Stars: 88
  • Forks: 29
  • Packages: 1
  • Downloads: 296
https://github.com/simonpenel/light_phylogeny

Light phylogeny API for Rust
horizontal-transfer newick phylogenetic-trees phylogenetics phylogeny phyloxml reconciled-tree recphyloxml rust svg
Added: over 1 year ago - Last Synced: about 1 year ago - Created: April 15, 2021

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: Rust
  • Commits: 401
  • Committers: 1
  • Issues: 1
  • Pull Requests: 0
  • Owner: simonpenel
  • Stars: 9
  • Forks: 0
  • Packages: 1
  • Downloads: 35,059
https://github.com/theosanderson/taxonium

A tool for exploring very large trees in the browser
deckgl phylogenetics phylogeny react tree virus
Added: over 1 year ago - Last Synced: about 1 year ago - Created: June 24, 2021

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: JavaScript
  • Commits: 2095
  • Committers: 13
  • Issues: 96
  • Pull Requests: 157
  • Owner: theosanderson
  • Stars: 93
  • Forks: 16
  • Packages: 2
  • Downloads: 575
https://github.com/jlsteenwyk/phykit

a UNIX shell toolkit for processing and analyzing multiple sequence alignments and phylogenies
bioinformatics evolution evolutionary-biology genomics multiple-sequence-alignments phylogenetics phylogenomics python
Added: over 1 year ago - Last Synced: about 1 year ago - Created: May 12, 2020

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: Python
  • Commits: 343
  • Committers: 8
  • Issues: 4
  • Pull Requests: 19
  • Owner: JLSteenwyk
  • Stars: 53
  • Forks: 7
  • Packages: 1
  • Downloads: 377
https://github.com/naturalis/barcode-constrained-phylogeny

Pipeline for building topologically-constrained phylogenies from DNA barcode data
dna-barcoding metabarcoding phylogenetic-diversity phylogenetic-placement phylogenetics
Added: over 1 year ago - Last Synced: about 1 year ago - Created: December 21, 2022

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: Python
  • Commits: 402
  • Committers: 7
  • Issues: 46
  • Pull Requests: 34
  • Owner: naturalis
  • Stars: 1
  • Forks: 3
  • Packages: 0
https://github.com/jlsteenwyk/clipkit

a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference
bioinformatics evolution evolutionary-biology genomics phylogenetics phylogenomics python systematics
Added: over 1 year ago - Last Synced: about 1 year ago - Created: April 11, 2020

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: Python
  • Commits: 266
  • Committers: 8
  • Issues: 17
  • Pull Requests: 35
  • Owner: JLSteenwyk
  • Stars: 54
  • Forks: 4
  • Packages: 1
  • Downloads: 480
https://github.com/nbisweden/mrbayes

MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. For documentation and downloading the program, please see the home page:
bayesian-inference bioinformatics markov-chain-monte-carlo phylogenetics research-tool
Added: over 1 year ago - Last Synced: about 1 year ago - Created: April 06, 2016

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: C
  • Commits: 1489
  • Committers: 18
  • Issues: 105
  • Pull Requests: 20
  • Owner: NBISweden
  • Stars: 222
  • Forks: 77
  • Packages: 1
  • Downloads: 101