sdellicour / seraphim
R package for studying environmental rasters and phylogenetic informed movements (Dellicour et al. 2016, Bioinformatics; Dellicour et al. 2016, BMC Bioinf.)
☆32Updated last month
Alternatives and similar repositories for seraphim:
Users that are interested in seraphim are comparing it to the libraries listed below
- Spatial Phylogenetic Reconstruction of Evolutionary Dynamics 3☆15Updated last year
- Reconstruction of transmission trees using genomic data☆61Updated last year
- Bayesian inference of ancestral dates on bacterial phylogenetic trees☆87Updated 5 months ago
- a pipeline for reconciliation of phylogenetic histories within a bacterial pangenome☆48Updated 2 years ago
- Phylogenetics between and within hosts at once, all along the genome.☆48Updated 5 months ago
- A fast approximation to a Dirichlet Process Mixture model (DPM) for clustering genetic data☆61Updated 2 years ago
- Phylodynamic inference☆18Updated 4 years ago
- Metagenomic Analysis in Real Time☆23Updated last week
- Sydney Phylogenetics Workshop☆63Updated 2 months ago
- Cluster Investigation & Virus Epidemiology Tool☆50Updated 2 years ago
- Virus reassortment inference software. Infers both recent and ancestral reassortment and uses flexible molecular clock constraints.☆12Updated last month
- Amplicon sequence processing workflow using QIIME 2 and Snakemake☆45Updated last month
- ☆54Updated last week
- ☆20Updated 2 years ago
- r package for post-clustering curation of amplicon next generation sequencing data (metabarcoding)☆64Updated last year
- AMPtk: Amplicon ToolKit for NGS data (formally UFITS)☆38Updated last year
- diversity estimation under ecological networks☆83Updated last year
- Course materials for the Genomics Aotearoa Metagenomics Summer School, to be hosted at the University of Auckland in Septermber☆55Updated 6 months ago
- SHallow shOtGUN profiler☆53Updated 3 years ago
- creating reference databases for amplicon sequencing☆34Updated this week
- Phylogenetic maximum representation sampling: choosing most representative strains or taxa☆37Updated 3 months ago
- A robust and fast clustering method for amplicon-based studies☆31Updated 2 years ago
- R We There Yet?☆30Updated 2 years ago
- Scalable relaxed clock phylogenetic dating☆24Updated 11 months ago
- A set of scripts for calculating pairwise SNP distance☆39Updated 2 years ago
- ☆35Updated last year
- Code for the paper "Learning the fitness dynamics of pathogens from phylogenies"☆15Updated this week
- A synthesis of bacterial and archaeal phenotypic trait data☆33Updated last year
- 🐻⇔🐨 Calculate distance matrix from ChewBBACA cgMLST allele call tables☆27Updated last year
- Tutorial on Bayesian phylogenetic analysis☆46Updated 7 years ago