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
• lh3 / psmc
  Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model
  ☆166Updated 2 years ago
• ksamuk / pixy
  Software for painlessly estimating average nucleotide diversity within and between populations
  ☆129Updated last week
• MesserLab / SLiM
  SLiM is a genetically explicit forward simulation software package for population genetics and evolutionary biology. It is highly flexib…
  ☆175Updated 3 weeks ago
• ANGSD / angsd
  Program for analysing NGS data.
  ☆236Updated 2 months ago
• edgardomortiz / vcf2phylip
  Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis
  ☆309Updated last year
• Dfam-consortium / RepeatMasker
  RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
  ☆252Updated this week
• tskit-dev / tsinfer
  Infer a tree sequence from genetic variation data.
  ☆59Updated last month
• Dfam-consortium / RepeatModeler
  De-Novo Repeat Discovery Tool
  ☆209Updated last week
• nf-core / eager
  A fully reproducible and state-of-the-art ancient DNA analysis pipeline
  ☆169Updated last week
• popgenmethods / smcpp
  SMC++ infers population history from whole-genome sequence data.
  ☆165Updated last year
• luntergroup / octopus
  Bayesian haplotype-based mutation calling
  ☆312Updated 2 months ago
• KamilSJaron / smudgeplot
  Inference of ploidy and heterozygosity structure using whole genome sequencing data
  ☆265Updated 2 months ago
• simonhmartin / genomics_general
  General tools for genomic analyses.
  ☆357Updated 2 months ago
• bedops / bedops
  BEDOPS: high-performance genomic feature operations
  ☆331Updated last week
• amkozlov / raxml-ng
  RAxML Next Generation: faster, easier-to-use and more flexible
  ☆422Updated this week
• VGP / vgp-assembly
  VGP repository for the genome assembly working group
  ☆193Updated last year
• millanek / Dsuite
  Fast calculation of Patterson's D (ABBA-BABA) and the f4-ratio statistics across many populations/species
  ☆171Updated 4 months ago
• mfumagalli / ngsTools
  Programs to analyse NGS data for population genetics purposes
  ☆174Updated 8 months ago
• fhcrc / seqmagick
  An imagemagick-like frontend to Biopython SeqIO
  ☆115Updated last year
• BGI-shenzhen / PopLDdecay
  PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format(VCF) files
  ☆190Updated 8 months ago
• schatzlab / genomescope
  Fast genome analysis from unassembled short reads
  ☆290Updated last year
• brentp / smoove
  structural variant calling and genotyping with existing tools, but, smoothly.
  ☆250Updated 10 months ago
• mossmatters / HybPiper
  Recovering genes from targeted sequence capture data
  ☆121Updated 4 months ago
• daler / gffutils
  GFF and GTF file manipulation and interconversion
  ☆299Updated last year
• isaacovercast / easySFS
  Effective selection of population size projection for construction of the site frequency spectrum. Convert VCF to dadi/fastsimcoal style …
  ☆149Updated 9 months ago
• mmatschiner / tutorials
  Tutorials on phylogenetic and phylogenomic inference
  ☆380Updated last year
• ndierckx / NOVOPlasty
  NOVOPlasty - The organelle assembler and heteroplasmy caller
  ☆187Updated last year
• rajanil / fastStructure
  A variational framework for inferring population structure from SNP genotype data.
  ☆136Updated 2 years ago