Alternatives and similar repositories for ipyrad

Users that are interested in ipyrad are comparing it to the libraries listed below

• enormandeau / stacks_workflow
  RADseq workflow using STACKS
  ☆59Updated last week
• mossmatters / HybPiper
  Recovering genes from targeted sequence capture data
  ☆128Updated 4 months ago
• simonhmartin / twisst
  Topology weighting by iterative sampling of sub-trees
  ☆81Updated 9 months ago
• darwintreeoflife / darwintreeoflife.data
  Interim data for the Darwin Tree of Life Project
  ☆33Updated 5 years ago
• AntonelliLab / seqcap_processor
  Bioinformatic pipeline for processing Sequence Capture data for Phylogenetics
  ☆22Updated 2 years ago
• speciationgenomics / speciationgenomics.github.io
  Repository for speciation genomics website
  ☆26Updated 2 months ago
• bpp / bpp
  Bayesian analysis of genomic sequence data under the multispecies coalescent model
  ☆106Updated 2 weeks ago
• mennodejong1986 / SambaR
  SambaR: Snp datA Management and Basic Analyses in R
  ☆31Updated 2 weeks ago
• tonig-evo / workshop-popgenome
  Tutorial about R package PopGenome
  ☆44Updated 6 years ago
• mrmckain / Fast-Plast
  Automated de novo assembly of whole chloroplast genomes.
  ☆47Updated last year
• esayyari / DiscoVista
  ☆42Updated 2 years ago
• CoBiG2 / RAD_Tools
  A collection of usefull tools for RAD or GBS data analysis
  ☆33Updated 7 months ago
• miriammiyagi / QuIBL
  Quantifying Introgression via Branch Lengths
  ☆54Updated 3 years ago
• LarsNauheimer / HybPhaser
  Workflow to detect and phase hybrids in target capture data
  ☆20Updated 2 years ago
• petrelharp / local_pca
  Methods for examining PCA locally along the genome.
  ☆85Updated last year
• fethalen / Patchwork
  Alignment-based retrieval and concatenation of phylogenetic markers from whole genome sequence (WGS) data
  ☆36Updated last year
• justincbagley / piranha
  Scripts for file processing and analysis in phylogenetics and phylogeography
  ☆13Updated 4 years ago
• millanek / fineRADstructure
  A package for population structure inference from RAD-seq data
  ☆34Updated 4 years ago
• millanek / Dsuite
  Fast calculation of Patterson's D (ABBA-BABA) and the f4-ratio statistics across many populations/species
  ☆179Updated 10 months ago
• rapidspeciation / biodiversity_genomics_course
  biodiversity genomics course by Nicol Rueda, Karin Näsvall and Joana Meier from the Wellcome Sanger Institute
  ☆57Updated 4 months ago
• mfoll / BayeScan
  Detecting natural selection from population-based genetic data
  ☆28Updated 6 years ago
• edgardomortiz / paralog-finder
  Detects and blacklists paralog RAD loci analyzed in Stacks or ipyrad, based on the McKinney 2017 method (doi:10.1111/1755-0998.12613)
  ☆10Updated 6 years ago
• mossmatters / phyloscripts
  Helper scripts for processing and visualization of phylogenetics datasets
  ☆30Updated last year
• speciationgenomics / presentations
  Presentations from the course
  ☆38Updated 2 years ago
• BGAcademy23 / smudgeplot
  Biodiversity Genomics Academy 2023: Understanding k-mers and ploidy using Smudgeplot
  ☆11Updated 2 years ago
• BenoitMorel / GeneRax
  ☆72Updated 4 months ago
• rhysf / Synima
  Synteny Imager
  ☆64Updated 3 months ago
• mmatschiner / snapp_prep
  Prepare XML input files for divergence-time estimation with SNAPP
  ☆19Updated 2 years ago
• nt246 / physalia-lcwgs
  Files for the the Physalia course on Population genomic inference from low-coverage whole-genome sequencing data, Oct 10-13, 2022
  ☆67Updated last week
• petrikemppainen / LDna
  LDna: an R package to perform linkage disequilibrium network analysis
  ☆31Updated last year