Alternatives and similar repositories for PopGenome

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

• jdalapicolla / LanGen_pipeline_version2

  View on GitHub
  Scripts in R for Landscape Genomics Analyses v.2
  ☆10Feb 17, 2023Updated 2 years ago
• speciationgenomics / scripts

  View on GitHub
  Scripts for analysis used during the course
  ☆93Apr 30, 2024Updated last year
• hardingnj / xpclr

  View on GitHub
  Code to compute the XP-CLR statistic to infer natural selection
  ☆102Jun 13, 2022Updated 3 years ago
• HMPNK / CSA2.6

  View on GitHub
  Chromosome Scale Assembler: A high-throughput chromosome scale genome assembly pipeline for vertebrate genomes
  ☆10Oct 16, 2024Updated last year
• awohns / unified_genealogy_paper

  View on GitHub
  A Unified Genealogy of Modern and Ancient Humans
  ☆20Dec 10, 2025Updated 2 months ago
• xinkaitong / 1k-pig-genomes

  View on GitHub
  Accurate haplotype construction and detection of selection signatures enabled by 889 high quality pig genome sequences
  ☆13May 11, 2023Updated 2 years ago
• adaptivegenome / repeatseq

  View on GitHub
  Accurate microsatellite genotypes from high-throughput resequencing data
  ☆24Sep 26, 2014Updated 11 years ago
• davidrasm / Espalier

  View on GitHub
  Espalier is a Python package for working with discordant phylogenetic trees using maximum agreement forests.
  ☆14Jul 19, 2023Updated 2 years ago
• bcm-uga / pcadapt

  View on GitHub
  Performing highly efficient genome scans for local adaptation with R package pcadapt v4
  ☆44Jul 25, 2025Updated 6 months ago
• ThomasTaus / poolSeq

  View on GitHub
  Analyze and simulate Pool-Seq time series data
  ☆17Jun 16, 2022Updated 3 years ago
• njdbickhart / GoatAssemblyScripts

  View on GitHub
  A loose collection of scripts and utilities for processing and analyzing the Goat reference genome assembly
  ☆11Feb 28, 2017Updated 8 years ago
• redsnic / WGA-LP

  View on GitHub
  A pipeline for whole genome assembly
  ☆16Apr 21, 2022Updated 3 years ago
• stevemussmann / BayesAss3-SNPs

  View on GitHub
  Modification of BayesAss 3.0.4 to allow handling of large SNP datasets
  ☆17Feb 19, 2022Updated 3 years ago
• Rosemeis / HaploNet

  View on GitHub
  Haplotype and population structure inference using neural networks.
  ☆28Dec 5, 2024Updated last year
• jingwanglab / Populus-Genomic-Consequences-of-Hybridization

  View on GitHub
  ☆16Jan 6, 2022Updated 4 years ago
• dyerlab / applied_population_genetics

  View on GitHub
  A textbook on population genetics
  ☆18Jan 7, 2026Updated last month
• champost / ABLE

  View on GitHub
  ABLE - Approximate Blockwise Likelihood Estimation
  ☆17Jul 4, 2018Updated 7 years ago
• btmartin721 / ClineHelpR

  View on GitHub
  Detects Outliers and plots genomic clines from BGC output, and extends the plotting functionality of INTROGRESS to Correlate genomic clin…
  ☆16Oct 12, 2024Updated last year
• grunwaldlab / poppr

  View on GitHub
  🌶 An R package for genetic analysis of populations with mixed (clonal/sexual) reproduction
  ☆72Sep 10, 2025Updated 5 months ago
• szpiech / selscan

  View on GitHub
  Haplotype based scans for selection
  ☆140Jan 6, 2026Updated last month
• simonhmartin / genomics_general

  View on GitHub
  General tools for genomic analyses.
  ☆386Feb 28, 2025Updated 11 months ago
• TorkamaniLab / imputation_accuracy_calculator

  View on GitHub
  ☆18Dec 15, 2021Updated 4 years ago
• wlz0726 / Population_Genomics_Scripts

  View on GitHub
  Scripts of population genomics analysis
  ☆36May 8, 2018Updated 7 years ago
• shapirolab / clineage

  View on GitHub
  ☆11Apr 21, 2023Updated 2 years ago
• alachins / raisd

  View on GitHub
  RAiSD: software to detect positive selection based on multiple signatures of a selective sweep and SNP vectors
  ☆37Nov 15, 2023Updated 2 years ago
• huangkang1987 / vcfpop

  View on GitHub
  ☆12Feb 16, 2025Updated 11 months ago
• joanam / scripts

  View on GitHub
  Scripts to handle NGS data and other biological data
  ☆22Jan 24, 2024Updated 2 years ago
• harrisonlab / popgen

  View on GitHub
  Population genetics analyses
  ☆23Oct 10, 2019Updated 6 years ago
• sudmantlab / loco-pipe

  View on GitHub
  loco-pipe is an automated Snakemake pipeline that streamlines a set of essential population genomic analyses for low-coverage whole genom…
  ☆29Jan 21, 2026Updated 3 weeks ago
• popgenmethods / smcpp

  View on GitHub
  SMC++ infers population history from whole-genome sequence data.
  ☆172Jan 20, 2024Updated 2 years ago
• liamrevell / learnPopGen

  View on GitHub
  initial commit
  ☆26Dec 29, 2022Updated 3 years ago
• alexlancaster / pypop

  View on GitHub
  PyPop: Python for Population Genomics
  ☆25Updated this week
• millanek / Dsuite

  View on GitHub
  Fast calculation of Patterson's D (ABBA-BABA) and the f4-ratio statistics across many populations/species
  ☆183Dec 19, 2024Updated last year
• tplinderoth / PopGenomicsTools

  View on GitHub
  Programs for performing various population genetic analyses
  ☆11Dec 2, 2024Updated last year
• fgvieira / badirate

  View on GitHub
  Estimating gene family turnover rates by likelihood-based methods
  ☆12Aug 17, 2020Updated 5 years ago
• cstubben / trinotateR

  View on GitHub
  Trinotate annotation report summaries in R
  ☆13Feb 24, 2016Updated 9 years ago
• futurefanzhang / Adaptation-to-climate-change-of-alfalfa

  View on GitHub
  This is the script used for analysis the population data of alfalfa
  ☆11May 22, 2024Updated last year
• Chemical118 / GDBr

  View on GitHub
  Genomic signature interpretation tool for DNA double-strand break repair mechanism
  ☆11Oct 8, 2025Updated 4 months ago
• therkildsen-lab / data-processing

  View on GitHub
  Scripts for going from raw .fastq files to processed and quality-checked .bam files for downstream analysis
  ☆14Nov 23, 2021Updated 4 years ago