phylogeography

evolbioinfo/pastml

Ancestral character reconstruction and visualisation for rooted phylogenetic trees

phylogeography/spread

Spread visualizes how viruses and other pathogens are spreading in time and space. It creates compellable shareable, interactive and time-animated visualization.

abschneider/StrainHub

Welcome to the StrainHub Repo - Files and Data - StrainHub Online:

justincbagley/piranha

Scripts for file processing and analysis in phylogenetics and phylogeography

tahiri-lab/aPhyloGeo

aPhyloGeo is a multiplatform application for the analysis of genetic and climatic conditions.

jdalapicolla/LanGen_pipeline_version2

Scripts in R for Landscape Genomics Analyses v.2

tahiri-lab/aPhyloGeo-pipeline

Phylogeographic workflow using sliding-windows, RAxML-NG and FastTree

V-Z/course-r-mol-data

R is nowadays probably the most powerful tool for calculations of all kinds. There are plenty of modules available for work with molecular data. Those will be introduced during the course.

ktmeaton/plague-phylogeography

Phylogeography of Yersinia pestis.

AKU-CITRIC-Center-for-Bioinformatics/ncov

Genomic Epidemiology of SARS-CoV-2 in Pakistan

evolbioinfo/phylocovid

folkehelseinstituttet/SARS-CoV-2_phylogeo

Phylogeographical analyses of SARS-CoV-2 variants of concern in Norway

gkarthik/zika-phylogeography

Zika Phylogeography

jdalapicolla/IBD_models.R

Scripts in R for analyses of Isolation by Distance (IBD) - PART 2 in LANDSCAPE GENOMICS PIPELINE

maxbiostat/FMDV_AMERICA

Tracking the spread of Foot-and-Mouth Disease virus in South America

ViennaRNA/CHIKV

Nextstrain community build 'Molecular epidemiology of Chikungunya virus'

ViennaRNA/VEEnext

Nextstrain community build 'Molecular epidemiology of Venezuelan equine encephalitis complex viruses'

adrianauscanga/TMVBarthropods

This is the repository for the project "Evaluating species origins within tropical sky-islands arthropod communities"

KAMarske/MarskeThomazKnowles_2020

R scripts for Marske et al 2020, Molecular Ecology

leonardslog/Tsirtalis_phylogeography

Supporting code for a study on the phylogeography of the common garter snake Thamnophis sirtalis

magnusnosnes/LineageHomology

LineageHomology uses phylogenies with reconstructed ancestral states to define groups of phylogenetic tips that have gained their states through homologous inheritance or de novo acquisition. LineageHomology can be applied to pathogen phylogeography to define transmission lineages and singletons and derive simple estimates of importation and local transmission (without regard to missing data).

NIH-BIGVI-PAKISTAN/ncov

Genomic epidemiology of novel coronavirus (SARS-CoV-2) in Pakistan

colbyford/BantuMigration

An Integrated Phylogeographic Analysis of the Bantu Migration

evolbioinfo/zika_Vietnam

Phylogeographic analyses of ZIKV

hernanmd/PhyloclassTalk

Phylogeographic text-mining platform

jdalapicolla/MLPE.R

Scripts in R for analyses of Isolation by Resistance (IBR) - PART 3 in LANDSCAPE GENOMICS PIPELINE

ktmeaton/plague-global-phylo-paper

Plague Global Phylogeny Manuscript