justincbagley / piranha
Scripts for file processing and analysis in phylogenetics and phylogeography
☆11Updated 3 years ago
Related projects ⓘ
Alternatives and complementary repositories for piranha
- A massively parallel tool for model selection and tree inference on thousands of genes☆41Updated 8 months ago
- This repository provides source code for several pipelines dedicated to the alignment of nucleotide coding sequences that are based on MA…☆32Updated last year
- Detects and blacklists paralog RAD loci analyzed in Stacks or ipyrad, based on the McKinney 2017 method (doi:10.1111/1755-0998.12613)☆10Updated 5 years ago
- Automated de novo assembly of whole chloroplast genomes.☆44Updated last month
- ☆21Updated 10 years ago
- Generates an NCBI .tbl file of annotations on a genome.☆64Updated 6 years ago
- Alignment-based retrieval and concatenation of phylogenetic markers from whole genome sequence (WGS) data☆34Updated 6 months ago
- A tool to identify and annotate homoplasies on a phylogeny and sequence alignment☆19Updated 3 years ago
- MCMCtreeR: A package to estimate distribution values for temporal node constraints and prepare input files for MCMCtree☆43Updated 4 years ago
- PREQUAL: a pre-alignment quality filter for comparative sequence analyses☆30Updated 2 years ago
- Implementation of the TreeShrink problem☆36Updated 2 months ago
- Tutorial about R package PopGenome☆40Updated 5 years ago
- Interim data for the Darwin Tree of Life Project☆32Updated 4 years ago
- An Efficient Swiss Army Knife for Population Genomic Analyses in R☆31Updated 5 months ago
- HyPhy standalone analyses☆38Updated 5 months ago
- Simple scripts for concatenate alignments and rename terminals for phylogenetics☆21Updated 2 years ago
- ☆24Updated 2 years ago
- EnTAP is moving to GitLab for future changes https://gitlab.com/PlantGenomicsLab/EnTAP☆37Updated last week
- Alignment-Based Sequence extraction☆14Updated 2 years ago
- ☆21Updated 5 years ago
- Tutorials on phylogenomic analyses for the ForBio Phylogenomics course☆30Updated 8 months ago
- Read, manipulate and visualize 'Pairwise mApping Format' data in R☆67Updated 3 years ago
- Whole-genome bioinformatic pipeline for pooled or individual-based NGS data using bash and R☆18Updated 2 years ago
- PoSeiDon: positive selection detection and recombination analysis pipeline☆35Updated 2 weeks ago
- PATO is a R package designed to analyze pangenomes (set of genomes) intra or inter species.☆58Updated last year
- R package for comparison of synteny conservation at the genome-wide scale.☆13Updated 5 months ago
- Repository for speciation genomics website☆24Updated 3 months ago
- Assembly by Reduced Complexity (ARC)☆41Updated 8 years ago
- A fast approximation to a Dirichlet Process Mixture model (DPM) for clustering genetic data☆58Updated 2 years ago
- STAG: Species Tree from All Genes☆31Updated 5 years ago