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30 repositories

dockerfiles
Public
Dockerfiles for tools commonly used for phylogenetic analyses
docker bioinformatics evolutionary
docker bioinformatics evolutionary
Dockerfile
•9•9•1•1•Updated Aug 10, 2026Aug 10, 2026
treesimulator
Public
Python
•
GNU General Public License v3.0
•2•6•0•0•Updated Jul 30, 2026Jul 30, 2026
phylodeep
Public
PhyloDeep is a python library for parameter estimation and model selection from phylogenetic trees, based on deep learning.
deep-learning phylodynamics
deep-learning phylodynamics
Python
•
Other
•7•30•5•1•Updated Jul 21, 2026Jul 21, 2026
gotree
Public
Gotree: a set of command line tools and an API to manipulate phylogenetic trees.
tree nexus tree-structure
tree nexus tree-structure newick phylogeny gotree itol
Go
•
GNU General Public License v2.0
•19•150•2•0•Updated Jul 15, 2026Jul 15, 2026
goalign
Public
Goalign : a set of command line tools and an API to manipulate multiple sequence alignments.
nexus alignment fasta
nexus alignment fasta phylogeny phylip phylip-alignment
Go
•
GNU General Public License v2.0
•8•90•0•0•Updated Jul 15, 2026Jul 15, 2026
pastml
Public
Ancestral character reconstruction and visualisation for rooted phylogenetic trees
visualisation phylogenetics phylogeography
visualisation phylogenetics phylogeography maximum-likelihood parsimony ancestral-character-reconstruction
Python
•
GNU General Public License v3.0
•8•42•10•0•Updated Apr 17, 2026Apr 17, 2026
bdct
Public
Birth-death epidemiological parameter estimator accounting for partner notification
Python
•
GNU General Public License v3.0
•0•3•0•0•Updated Feb 24, 2026Feb 24, 2026
condor
Public
ConDor: a workflow to detect convergent evolution in large protein alignments
Python
•3•5•0•0•Updated Jan 13, 2026Jan 13, 2026
bdei
Public
Birth-Death Exposed-Infectious (BDEI) model parameter inference from phylogenetic trees
Python
•
GNU Lesser General Public License v2.1
•0•5•0•0•Updated Apr 14, 2025Apr 14, 2025
bayesian_bootstrap_analyses
Public
Nextflow
•0•2•0•0•Updated Sep 20, 2024Sep 20, 2024
geo_subsampler
Public
A phylogeny subsampling tool combining geographic proportions and phylogenetic diversity
Python
•
GNU General Public License v3.0
•0•3•0•0•Updated Sep 6, 2024Sep 6, 2024
phylodeep_data_bdss
Public
Data needed for CI computation with Birth-Death model with superspreading (BDSS) in [PhyloDeep](https://github.com/evolbioinfo/phylodeep)
Python
•
Other
•0•0•0•0•Updated Aug 6, 2024Aug 6, 2024
phylodeep_data_bdei
Public
Data needed for CI computation with Birth-Death Exposed-Infectious (BDEI) model in [PhyloDeep](https://github.com/evolbioinfo/phylodeep).
Python
•
Other
•0•0•0•0•Updated Aug 1, 2024Aug 1, 2024
phylodeep_data_bd
Public
Data needed for CI computation with Birth-Death (BDEI) model in [PhyloDeep](https://github.com/evolbioinfo/phylodeep).
Python
•
Other
•0•0•0•0•Updated Aug 1, 2024Aug 1, 2024
bayesian_bootstrap
Public
Nextflow
•0•0•0•0•Updated Jun 25, 2024Jun 25, 2024
pastmlweb
Public
Web-app for PastML
CSS
•
GNU General Public License v3.0
•0•1•0•0•Updated May 24, 2024May 24, 2024
condor-analysis
Public
Files and scripts from ConDor analysis
Jupyter Notebook
•1•1•0•0•Updated Jan 28, 2024Jan 28, 2024
HIV1-UK
Public
Analysis of drug resistance mutation patterns in the UK
HTML
•0•0•0•0•Updated Dec 19, 2023Dec 19, 2023
booster-web
Public
booster-web
bootstrap golang transfer
bootstrap golang transfer webapp phylogeny booster
Go
•
GNU General Public License v2.0
•0•2•0•0•Updated Apr 19, 2023Apr 19, 2023
phylocovid
Public
phylogenetics phylogeography covid-19
phylogenetics phylogeography covid-19
HTML
•
GNU General Public License v3.0
•0•3•0•0•Updated Apr 12, 2022Apr 12, 2022
HIV1-CRF19_Cuba
Public
Phylogenetic analyses of CRF19 spread in Cuba and worldwide
Python
•
GNU General Public License v3.0
•0•0•0•0•Updated Dec 4, 2021Dec 4, 2021
gotree_usecase
Public
Nextflow
•
GNU General Public License v2.0
•0•0•0•0•Updated Aug 24, 2021Aug 24, 2021
lsd-web
Public
phylogenetics epidemiology
phylogenetics epidemiology
HTML
•
GNU General Public License v2.0
•0•0•0•1•Updated Jun 10, 2021Jun 10, 2021
zika_Vietnam
Public
Phylogeographic analyses of ZIKV
phylogeography zika zika-virus
phylogeography zika zika-virus
HTML
•0•0•0•0•Updated Apr 8, 2021Apr 8, 2021
jphmm_tools
Public
Methods for extracting information from jpHMM (http://jphmm.gobics.de) output.
hiv recombination subtyping
hiv recombination subtyping
Python
•
GNU General Public License v3.0
•0•0•0•0•Updated Mar 25, 2021Mar 25, 2021
HIV_SA
Public
Python
•0•0•0•0•Updated Nov 13, 2020Nov 13, 2020
booster
Public
support bootstrap phylogenetics
support bootstrap phylogenetics
C
•
GNU General Public License v2.0
•1•28•2•0•Updated May 22, 2020May 22, 2020
indelible
Public
C++
•1•0•2•0•Updated Sep 18, 2019Sep 18, 2019
cytopast
Public archive
cytopast is a python3 module that creates zoomable HTML visualisation of phylogenetic trees with annotated nodes
visualization visualisation phylogenetics
visualization visualisation phylogenetics ancestral-inference
Python
•
GNU General Public License v3.0
•0•2•3•0•Updated Nov 22, 2018Nov 22, 2018
booster-workflows
Public
bootstrap nextflow phylogenetics
bootstrap nextflow phylogenetics workflows booster
Nextflow
•0•2•0•0•Updated Apr 3, 2018Apr 3, 2018

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Evolutionary Bioinformatics

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All

30 repositories

dockerfiles

treesimulator

phylodeep

gotree

goalign

pastml

bdct

condor

bdei

bayesian_bootstrap_analyses

geo_subsampler

phylodeep_data_bdss

phylodeep_data_bdei

phylodeep_data_bd

bayesian_bootstrap

pastmlweb

condor-analysis

HIV1-UK

booster-web

phylocovid

HIV1-CRF19_Cuba

gotree_usecase

lsd-web

zika_Vietnam

jphmm_tools

HIV_SA

booster

indelible

cytopast

booster-workflows

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30 repositories