tahiri-lab/aPhyloGeo

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

Language: Python - Size: 74.9 MB - Last synced at: 2 days ago - Pushed at: 12 days ago - Stars: 10 - Forks: 8

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).

Language: R - Size: 12.6 MB - Last synced at: 15 days ago - Pushed at: 15 days ago - Stars: 0 - Forks: 0

shawnlaffan/biodiverse

A tool for the spatial analysis of diversity

Language: Perl - Size: 452 MB - Last synced at: 7 days ago - Pushed at: about 2 months ago - Stars: 77 - Forks: 19

ktmeaton/plague-phylogeography

Phylogeography of Yersinia pestis.

Language: Jupyter Notebook - Size: 634 MB - Last synced at: 3 days ago - Pushed at: 8 months ago - Stars: 8 - Forks: 2

phylogeography/spread

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

Language: Clojure - Size: 21.5 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 18 - Forks: 0

evolbioinfo/pastml

Ancestral character reconstruction and visualisation for rooted phylogenetic trees

Language: Python - Size: 35.9 MB - Last synced at: 6 days ago - Pushed at: 3 months ago - Stars: 32 - Forks: 6

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.

Language: TeX - Size: 1.46 GB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 8 - Forks: 4

JBris/beast2-experiments

Experiments with the BEAST 2 software

Language: Python - Size: 34.9 MB - Last synced at: 26 days ago - Pushed at: 4 months ago - Stars: 1 - Forks: 0

JBris/beast2-docker

Docker and Apptainer setup for the BEAST 2 software

Language: R - Size: 679 KB - Last synced at: 26 days ago - Pushed at: 4 months ago - Stars: 1 - Forks: 0

abschneider/StrainHub

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

Language: HTML - Size: 10.8 MB - Last synced at: 9 months ago - Pushed at: almost 3 years ago - Stars: 14 - Forks: 4

evolbioinfo/phylocovid

Language: HTML - Size: 19.6 MB - Last synced at: 11 months ago - Pushed at: about 3 years ago - Stars: 3 - Forks: 0

ViennaRNA/CHIKV

Nextstrain community build 'Molecular epidemiology of Chikungunya virus'

Size: 3.94 MB - Last synced at: about 1 year ago - Pushed at: over 2 years ago - Stars: 1 - Forks: 1

jdalapicolla/LanGen_pipeline_version2

Scripts in R for Landscape Genomics Analyses v.2

Language: R - Size: 130 KB - Last synced at: over 1 year ago - Pushed at: about 2 years ago - Stars: 5 - Forks: 5

jdalapicolla/IBD_models.R

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

Language: R - Size: 69.3 KB - Last synced at: over 1 year ago - Pushed at: about 2 years ago - Stars: 1 - Forks: 1

ViennaRNA/VEEnext

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

Size: 1.6 MB - Last synced at: about 1 year ago - Pushed at: over 2 years ago - Stars: 1 - Forks: 1

tahiri-lab/aPhyloGeo-pipeline

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

Language: Python - Size: 3.39 MB - Last synced at: about 2 years ago - Pushed at: about 2 years ago - Stars: 3 - Forks: 0

jdalapicolla/MLPE.R

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

Language: R - Size: 113 KB - Last synced at: about 1 year ago - Pushed at: about 2 years ago - Stars: 0 - Forks: 2

AKU-CITRIC-Center-for-Bioinformatics/ncov

Genomic Epidemiology of SARS-CoV-2 in Pakistan

Size: 57.2 MB - Last synced at: 5 months ago - Pushed at: over 1 year ago - Stars: 3 - Forks: 0

maxbiostat/FMDV_AMERICA

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

Language: Jupyter Notebook - Size: 114 MB - Last synced at: 1 day ago - Pushed at: over 2 years ago - Stars: 1 - Forks: 0

folkehelseinstituttet/SARS-CoV-2_phylogeo

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

Language: R - Size: 99 MB - Last synced at: about 1 year ago - Pushed at: about 3 years ago - Stars: 3 - Forks: 0

justincbagley/piranha

Scripts for file processing and analysis in phylogenetics and phylogeography

Language: Shell - Size: 13.7 MB - Last synced at: over 1 year ago - Pushed at: over 4 years ago - Stars: 10 - Forks: 3

ktmeaton/plague-global-phylo-paper

Plague Global Phylogeny Manuscript

Language: HTML - Size: 9.22 MB - Last synced at: 3 days ago - Pushed at: almost 4 years ago - Stars: 0 - Forks: 0

adrianauscanga/TMVBarthropods

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

Language: HTML - Size: 24.6 MB - Last synced at: over 1 year ago - Pushed at: about 4 years ago - Stars: 0 - Forks: 0

evolbioinfo/zika_Vietnam

Phylogeographic analyses of ZIKV

Language: HTML - Size: 8 MB - Last synced at: almost 2 years ago - Pushed at: about 4 years ago - Stars: 0 - Forks: 0

gkarthik/zika-phylogeography

Zika Phylogeography

Language: HTML - Size: 5.61 MB - Last synced at: almost 2 years ago - Pushed at: over 7 years ago - Stars: 1 - Forks: 1

colbyford/BantuMigration

An Integrated Phylogeographic Analysis of the Bantu Migration

Language: HTML - Size: 302 MB - Last synced at: about 2 years ago - Pushed at: almost 5 years ago - Stars: 0 - Forks: 0

hernanmd/PhyloclassTalk

Phylogeographic text-mining platform

Size: 0 Bytes - Last synced at: 2 months ago - Pushed at: about 8 years ago - Stars: 0 - Forks: 0