phylogeography / SpreaD3Links
Spatial Phylogenetic Reconstruction of Evolutionary Dynamics 3
☆15Updated 2 years ago
Alternatives and similar repositories for SpreaD3
Users that are interested in SpreaD3 are comparing it to the libraries listed below
Sorting:
- R package for studying environmental rasters and phylogenetic informed movements (Dellicour et al. 2016, Bioinformatics; Dellicour et al.…☆34Updated 2 months ago
- Scalable relaxed clock phylogenetic dating☆25Updated last year
- Reconstruction of transmission trees using genomic data☆62Updated last year
- Code for the paper "Learning the fitness dynamics of pathogens from phylogenies"☆18Updated last month
- A fast approximation to a Dirichlet Process Mixture model (DPM) for clustering genetic data☆62Updated 2 years ago
- Virus reassortment inference software. Infers both recent and ancestral reassortment and uses flexible molecular clock constraints.☆15Updated last month
- a pipeline for reconciliation of phylogenetic histories within a bacterial pangenome☆49Updated 2 years ago
- ☆17Updated this week
- R package for microbial pangenomics☆23Updated 3 years ago
- Bayesian inference of ancestral dates on bacterial phylogenetic trees☆88Updated 2 weeks ago
- R We There Yet?☆30Updated 2 months ago
- Sydney Phylogenetics Workshop☆62Updated 5 months ago
- Phylogenetics between and within hosts at once, all along the genome.☆48Updated 8 months ago
- A robust and fast clustering method for amplicon-based studies☆31Updated 2 years ago
- Spatial Phylogenetic Reconstruction of Evolutionary Dynamics☆20Updated 6 years ago
- ☆21Updated 2 years ago
- A tool to identify and annotate homoplasies on a phylogeny and sequence alignment☆20Updated 4 years ago
- AMPtk: Amplicon ToolKit for NGS data (formally UFITS)☆38Updated last year
- Influenza data pipeline to automate genotyping assignment☆33Updated this week
- A set of R scripts for the analysis of microbial profiles☆41Updated last year
- ☆26Updated 4 years ago
- BEAST 2 package which provides support for multi-type trees: phylogenetic trees on structured populations.☆21Updated 3 months ago
- Metagenomic Analysis in Real Time☆24Updated last week
- functions for analyzing phyloseq data☆27Updated 4 months ago
- A pipeline for performing genome-wide association tests for bacterial genomes.☆27Updated 7 years ago
- An R package for analysis of microbiome relative abundance data using zero inflated beta GAMLSS and meta-analysis across microbiome studi…☆33Updated 4 years ago
- Experimental pipeline to perform de novo PICRUSt on de-noised amplicon sequence variants (ASV)☆19Updated 6 years ago
- A versatile simulation engine for stochastic population dynamics models.☆22Updated 2 years ago
- Simple scripts for concatenate alignments and rename terminals for phylogenetics☆21Updated 2 years ago
- Using ggtree to build phylogenetic trees☆47Updated 7 months ago