Alternatives and similar repositories for msprime

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

• popsim-consortium / stdpopsim
  A library of standard population genetic models
  ☆133Updated this week
• tskit-dev / tskit
  Population-scale Ancestral Recombination Graph (ARG) library
  ☆162Updated last week
• ksamuk / pixy
  Software for painlessly estimating average nucleotide diversity within and between populations
  ☆132Updated last month
• lh3 / psmc
  Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model
  ☆166Updated 2 years ago
• simonhmartin / genomics_general
  General tools for genomic analyses.
  ☆362Updated 3 months ago
• MesserLab / SLiM
  SLiM is a genetically explicit forward simulation software package for population genetics and evolutionary biology. It is highly flexib…
  ☆177Updated last week
• edgardomortiz / vcf2phylip
  Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis
  ☆312Updated last year
• KamilSJaron / smudgeplot
  Inference of ploidy and heterozygosity structure using whole genome sequencing data
  ☆269Updated 2 weeks ago
• Cibiv / IQ-TREE
  Efficient phylogenomic software by maximum likelihood
  ☆202Updated 3 years ago
• amkozlov / raxml-ng
  RAxML Next Generation: faster, easier-to-use and more flexible
  ☆427Updated 2 weeks ago
• ANGSD / angsd
  Program for analysing NGS data.
  ☆236Updated 3 months ago
• millanek / Dsuite
  Fast calculation of Patterson's D (ABBA-BABA) and the f4-ratio statistics across many populations/species
  ☆172Updated 5 months ago
• popgenmethods / smcpp
  SMC++ infers population history from whole-genome sequence data.
  ☆168Updated last year
• rajanil / fastStructure
  A variational framework for inferring population structure from SNP genotype data.
  ☆136Updated 2 years ago
• iqtree / iqtree2
  IQ-TREE software version 2: phylogenetics by maximum likelihood
  ☆285Updated last month
• Dfam-consortium / RepeatMasker
  RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
  ☆256Updated 3 weeks ago
• marekborowiec / AMAS
  Calculate summary statistics and manipulate multiple sequence alignments
  ☆84Updated last year
• nf-core / eager
  A fully reproducible and state-of-the-art ancient DNA analysis pipeline
  ☆169Updated this week
• neherlab / treetime
  Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction
  ☆242Updated 2 weeks ago
• mossmatters / HybPiper
  Recovering genes from targeted sequence capture data
  ☆123Updated 4 months ago
• DReichLab / EIG
  Eigen tools by Nick Patterson and Alkes Price lab
  ☆184Updated last year
• BGI-shenzhen / PopLDdecay
  PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format(VCF) files
  ☆192Updated 9 months ago
• Gaius-Augustus / Augustus
  Genome annotation with AUGUSTUS
  ☆304Updated 5 months ago
• mfumagalli / ngsTools
  Programs to analyse NGS data for population genetics purposes
  ☆174Updated 9 months ago
• isaacovercast / easySFS
  Effective selection of population size projection for construction of the site frequency spectrum. Convert VCF to dadi/fastsimcoal style …
  ☆151Updated 9 months ago
• Dfam-consortium / RepeatModeler
  De-Novo Repeat Discovery Tool
  ☆214Updated last month
• mmatschiner / tutorials
  Tutorials on phylogenetic and phylogenomic inference
  ☆383Updated last year
• cggh / scikit-allel
  A Python package for exploring and analysing genetic variation data
  ☆296Updated last month
• HadrienG / InSilicoSeq
  A sequencing simulator
  ☆198Updated 2 months ago
• schatzlab / genomescope
  Fast genome analysis from unassembled short reads
  ☆289Updated last year