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bayesian_bootstrap

bayesian_bootstrap_analyses

bdei

Birth-Death Exposed-Infectious (BDEI) model parameter inference from phylogenetic trees

booster

booster-web

booster-web

booster-workflows

condor

ConDor: a workflow to detect convergent evolution in large protein alignments

condor-analysis

Files and scripts from ConDor analysis

cytopast

cytopast is a python3 module that creates zoomable HTML visualisation of phylogenetic trees with annotated nodes

dockerfiles

Dockerfiles for tools commonly used for phylogenetic analyses

geo_subsampler

A phylogeny subsampling tool combining geographic proportions and phylogenetic diversity

goalign

Goalign is a set of command line tools and an API to manipulate multiple sequence alignments. It is implemented in Go language.

gotree

Gotree is a set of command line tools and an API to manipulate phylogenetic trees. It is implemented in Go language.

gotree_usecase

hiv1-crf19_cuba

Phylogenetic analyses of CRF19 spread in Cuba and worldwide

hiv1-uk

Analysis of drug resistance mutation patterns in the UK

hiv_sa

indelible

jphmm_tools

Methods for extracting information from jpHMM (http://jphmm.gobics.de) output.

lsd-web

pastml

Ancestral character reconstruction and visualisation for rooted phylogenetic trees

pastmlweb

Web-app for PastML

phylocovid

phylodeep

PhyloDeep is a python library for parameter estimation and model selection from phylogenetic trees, based on deep learning.

phylodeep_data_bd

Data needed for CI computation with Birth-Death (BDEI) model in [PhyloDeep](https://github.com/evolbioinfo/phylodeep).

phylodeep_data_bdei

Data needed for CI computation with Birth-Death Exposed-Infectious (BDEI) model in [PhyloDeep](https://github.com/evolbioinfo/phylodeep).

phylodeep_data_bdss

Data needed for CI computation with Birth-Death model with superspreading (BDSS) in [PhyloDeep](https://github.com/evolbioinfo/phylodeep)

treesimulator

zika_vietnam

Phylogeographic analyses of ZIKV