Evolutionary Bioinformatics

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30 repositories

treesimulator
Public
Python
•
GNU General Public License v3.0
•1•2•0•0•Updated Dec 18, 2024Dec 18, 2024
bdpn
Public
Birth-death epidemiological parameter estimator accounting for partner notification
Python
•
GNU General Public License v3.0
•0•1•0•0•Updated Nov 29, 2024Nov 29, 2024
dockerfiles
Public
Dockerfiles for tools commonly used for phylogenetic analyses
bioinformatics evolutionary docker
Dockerfile
•9•9•1•0•Updated Nov 19, 2024Nov 19, 2024
phylodeep
Public
PhyloDeep is a python library for parameter estimation and model selection from phylogenetic trees, based on deep learning.
phylodynamics deep-learning
Python
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Other
•6•23•3•1•Updated Oct 9, 2024Oct 9, 2024
gotree
Public
Gotree is a set of command line tools and an API to manipulate phylogenetic trees. It is implemented in Go language.
tree tree-structure phylogeny nexus newick gotree itol
Go
•
GNU General Public License v2.0
•16•125•6•0•Updated Sep 26, 2024Sep 26, 2024
goalign
Public
Goalign is a set of command line tools and an API to manipulate multiple sequence alignments. It is implemented in Go language.
nexus alignment fasta phylogeny phylip phylip-alignment
Go
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GNU General Public License v2.0
•8•74•2•0•Updated Sep 26, 2024Sep 26, 2024
bayesian_bootstrap_analyses
Public
Nextflow
•0•2•0•0•Updated Sep 20, 2024Sep 20, 2024
pastml
Public
Ancestral character reconstruction and visualisation for rooted phylogenetic trees
visualisation phylogenetics phylogeography maximum-likelihood parsimony ancestral-character-reconstruction
Python
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GNU General Public License v3.0
•6•32•11•0•Updated Sep 18, 2024Sep 18, 2024
geo_subsampler
Public
A phylogeny subsampling tool combining geographic proportions and phylogenetic diversity
Python
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GNU General Public License v3.0
•0•0•0•0•Updated Sep 6, 2024Sep 6, 2024
bdei
Public
Birth-Death Exposed-Infectious (BDEI) model parameter inference from phylogenetic trees
Python
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GNU Lesser General Public License v2.1
•0•3•0•0•Updated Aug 7, 2024Aug 7, 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
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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
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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
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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
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GNU General Public License v3.0
•0•1•0•0•Updated May 24, 2024May 24, 2024
condor
Public
ConDor: a workflow to detect convergent evolution in large protein alignments
Python
•3•2•0•0•Updated Jan 29, 2024Jan 29, 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 webapp phylogeny booster
Go
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GNU General Public License v2.0
•0•1•0•0•Updated Apr 19, 2023Apr 19, 2023
phylocovid
Public
phylogenetics phylogeography covid-19
HTML
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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
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GNU General Public License v3.0
•0•0•0•0•Updated Dec 4, 2021Dec 4, 2021
gotree_usecase
Public
Nextflow
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GNU General Public License v2.0
•0•0•0•0•Updated Aug 24, 2021Aug 24, 2021
lsd-web
Public
phylogenetics epidemiology
HTML
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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-virus zika
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
Python
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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
C
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GNU General Public License v2.0
•2•27•2•0•Updated May 22, 2020May 22, 2020
indelible
Public
C++
•1•0•1•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 ancestral-inference
Python
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GNU General Public License v3.0
•0•2•3•0•Updated Nov 22, 2018Nov 22, 2018
booster-workflows
Public
bootstrap nextflow phylogenetics workflows booster
Nextflow
•0•1•0•0•Updated Apr 3, 2018Apr 3, 2018