Alternatives and similar repositories for SLiM

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

• tskit-dev / msprime
  Simulate genealogical trees and genomic sequence data using population genetic models
  ☆193Updated last month
• popsim-consortium / stdpopsim
  A library of standard population genetic models
  ☆134Updated last month
• lh3 / psmc
  Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model
  ☆170Updated 2 years ago
• ksamuk / pixy
  Software for painlessly estimating average nucleotide diversity within and between populations
  ☆138Updated 2 months ago
• mfumagalli / ngsTools
  Programs to analyse NGS data for population genetics purposes
  ☆175Updated 10 months ago
• mossmatters / HybPiper
  Recovering genes from targeted sequence capture data
  ☆126Updated 2 weeks ago
• jade-cheng / ohana
  mixture classification, constraint optimization, outlier detection, population structure, admixture history, and selection detection.
  ☆87Updated 4 years ago
• pierrebarbera / epa-ng
  Massively parallel phylogenetic placement of genetic sequences
  ☆84Updated 2 years ago
• Cibiv / IQ-TREE
  Efficient phylogenomic software by maximum likelihood
  ☆202Updated 3 years ago
• JimWhiting91 / genotype_plot
  A set of functions to visualise genotypes based on a VCF
  ☆86Updated 3 years ago
• bpp / bpp
  Bayesian analysis of genomic sequence data under the multispecies coalescent model
  ☆100Updated last month
• voichek / kmersGWAS
  A library for running k-mers based GWAS
  ☆110Updated 8 months ago
• chasewnelson / SNPGenie
  Program for estimating πN/πS, dN/dS, and other diversity measures from next-generation sequencing data
  ☆115Updated last year
• tseemann / any2fasta
  Convert various sequence formats to FASTA
  ☆136Updated 3 years ago
• FePhyFoFum / phyx
  phylogenetics tools for linux (and other mostly posix compliant) computers
  ☆119Updated 6 months ago
• ANGSD / angsd
  Program for analysing NGS data.
  ☆238Updated 4 months ago
• popgenmethods / smcpp
  SMC++ infers population history from whole-genome sequence data.
  ☆168Updated last year
• MesserLab / SLiM-Extras
  Extra add-ons that may be useful for people using SLiM, but that are not part of the SLiM project itself
  ☆43Updated 3 months ago
• David-Peede / BIOL1435
  Resources for Brown University's BIOL 1435 course.
  ☆20Updated last year
• millanek / Dsuite
  Fast calculation of Patterson's D (ABBA-BABA) and the f4-ratio statistics across many populations/species
  ☆175Updated 7 months ago
• xavierdidelot / ClonalFrameML
  ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes
  ☆115Updated last year
• tskit-dev / tskit
  Population-scale Ancestral Recombination Graph (ARG) library
  ☆164Updated this week
• ddarriba / jmodeltest2
  Automatically exported from code.google.com/p/jmodeltest2
  ☆80Updated 3 years ago
• dipetkov / eems
  Estimating Effective Migration Surfaces
  ☆103Updated last year
• rajanil / fastStructure
  A variational framework for inferring population structure from SNP genotype data.
  ☆139Updated 2 years ago
• jtlovell / GENESPACE
  ☆212Updated 5 months ago
• moiexpositoalonsolab / grenepipe
  A flexible, scalable, and reproducible pipeline to automate variant calling from raw sequence reads, with lots of bells and whistles - fo…
  ☆102Updated 3 weeks ago
• jpuritz / dDocent
  a bash pipeline for RAD sequencing
  ☆55Updated 5 months ago
• bodkan / slendr
  Population genetic simulations in R 🌍
  ☆59Updated last week
• conchoecia / odp
  oxford dot plots
  ☆156Updated 3 weeks ago