Alternatives and similar repositories for treeseq-inference

Users that are interested in treeseq-inference are comparing it to the libraries listed below

• popsim-consortium / analysis

  View on GitHub
  Analysis of inference methods on standard population models
  ☆25Dec 3, 2021Updated 4 years ago
• standard-aaron / palm

  View on GitHub
  Polygenic Adaptation Likelihood Method - Inferring natural selection on complex traits from whole-genome genealogies
  ☆16Nov 13, 2020Updated 5 years ago
• bobverity / MavericK

  View on GitHub
  Source code for the program MavericK, described fully at www.bobverity.com/maverick
  ☆12Jun 21, 2018Updated 7 years ago
• adigenova / fast-sg

  View on GitHub
  Fast-SG: An alignment-free algorithm for ultrafast scaffolding graph construction from short or long reads.
  ☆22May 29, 2018Updated 7 years ago
• owensgl / reformat

  View on GitHub
  Scripts for reformatting data. Mainly from tab separated to an esoteric program specific format
  ☆13Feb 21, 2025Updated 11 months ago
• kdm9 / kWIP

  View on GitHub
  De novo estimates of genetic relatedness from next-gen sequencing data
  ☆45Jul 28, 2019Updated 6 years ago
• andrewkern / biol610

  View on GitHub
  intro to programming for IE2 evolution students
  ☆12Jan 31, 2024Updated 2 years ago
• halasadi / MAPS

  View on GitHub
  software for the MAPS method
  ☆25Mar 20, 2019Updated 6 years ago
• bwringe / hybriddetective

  View on GitHub
  ☆15Mar 20, 2023Updated 2 years ago
• Schraiber / selection

  View on GitHub
  ☆15Jul 17, 2019Updated 6 years ago
• bcm-uga / TESS3_encho_sen

  View on GitHub
  TESS3 is a fast and efficient program for estimating spatial population structure based on geographically constrained non-negative matrix…
  ☆21Jun 21, 2023Updated 2 years ago
• danjlawson / badMIXTURE

  View on GitHub
  R package for comparing mixture solutions to similarity data, with a focus STRUCTURE like models to ChromoPainter palettes
  ☆30Sep 27, 2019Updated 6 years ago
• paula-tataru / polyDFE

  View on GitHub
  predicting DFE and alpha from polymorphism data
  ☆28Oct 4, 2018Updated 7 years ago
• ruiguo-bio / replong

  View on GitHub
  source code of the paper "RepLong - de novo repeat discovery from long reads"
  ☆18Jan 4, 2025Updated last year
• Rosemeis / HaploNet

  View on GitHub
  Haplotype and population structure inference using neural networks.
  ☆28Dec 5, 2024Updated last year
• jade-cheng / ohana

  View on GitHub
  mixture classification, constraint optimization, outlier detection, population structure, admixture history, and selection detection.
  ☆88Jun 14, 2021Updated 4 years ago
• champost / ABLE

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

  View on GitHub
  Fast inference of fine-scale recombination rates based on fused-LASSO
  ☆55Updated this week
• DecodeGenetics / popSTR

  View on GitHub
  PopSTR - A Population based microsatellite genotyper
  ☆32Oct 23, 2023Updated 2 years ago
• kr-colab / locator

  View on GitHub
  deep learning prediction of geographic location from individual genome sequences
  ☆52Jan 20, 2025Updated last year
• pblischak / polyploid-genotyping

  View on GitHub
  SNP genotyping in polyploids
  ☆17Aug 12, 2020Updated 5 years ago
• mcveanlab / TreeWAS

  View on GitHub
  ☆16Oct 16, 2017Updated 8 years ago
• LohmuellerLab / fitdadi

  View on GitHub
  Tools for inference of the DFE with dadi
  ☆14Apr 16, 2021Updated 4 years ago
• grenaud / schmutzi

  View on GitHub
  Maximum a posteriori estimate of contamination for ancient samples
  ☆23Nov 4, 2025Updated 3 months ago
• sriramlab / ArchIE

  View on GitHub
  A statistical framework for reference-free inference of archaic local ancestry
  ☆16Nov 8, 2019Updated 6 years ago
• poruloh / Eagle

  View on GitHub
  Haplotype phasing software
  ☆69Dec 5, 2020Updated 5 years ago
• popsim-consortium / demes-python

  View on GitHub
  Tools for describing and manipulating demographic models.
  ☆19May 18, 2025Updated 8 months ago
• tvkent / GERPplusplus

  View on GitHub
  GERP++ code from Sidow Lab modified by Kevin Thornton to compile properly.
  ☆25Sep 19, 2016Updated 9 years ago
• samebdon / heRho

  View on GitHub
  heterozygosity-based estimator of Rho - https://academic.oup.com/genetics/advance-article/doi/10.1093/genetics/iyac100/6623412
  ☆10Aug 24, 2025Updated 5 months ago
• ZhiGroup / Syllable-PBWT

  View on GitHub
  ☆12Aug 23, 2023Updated 2 years ago
• andrewkern / popGenMachineLearningExamples

  View on GitHub
  simple examples of using supervised machine learning for population genetics inference
  ☆39Oct 26, 2017Updated 8 years ago
• scrm / scrm

  View on GitHub
  A coalescent simulator for genome-scale sequences
  ☆44Jan 2, 2024Updated 2 years ago
• gwct / referee

  View on GitHub
  Reference genome quality scores
  ☆20Dec 17, 2020Updated 5 years ago
• wf8 / homologizer

  View on GitHub
  Homologizer: phasing gene copies into polyploid subgenomes
  ☆11Feb 3, 2026Updated last week
• ngs-docs / 2015-shell-genomics

  View on GitHub
  Lesson for the shell for genomics
  ☆10Jan 12, 2021Updated 5 years ago
• malthesr / winsfs

  View on GitHub
  Site frequency spectrum estimation based on window expectation-maximisation algorithm
  ☆14May 19, 2023Updated 2 years ago
• rivasiker / trails

  View on GitHub
  Tree reconstruction of ancestry using incomplete lineage sorting
  ☆11Jan 9, 2026Updated last month
• mturchin20 / bmass

  View on GitHub
  R package for 'Bayesian multivariate analysis of summary statistics' (Stephens Lab)
  ☆10Sep 17, 2020Updated 5 years ago
• tplinderoth / PopGenomicsTools

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