tskit-dev / msprimeLinks
Simulate genealogical trees and genomic sequence data using population genetic models
☆199Updated last week
Alternatives and similar repositories for msprime
Users that are interested in msprime are comparing it to the libraries listed below
Sorting:
- A library of standard population genetic models☆136Updated last week
- Population-scale Ancestral Recombination Graph (ARG) library☆171Updated this week
- SLiM is a genetically explicit forward simulation software package for population genetics and evolutionary biology. It is highly flexib…☆188Updated last week
- Programs to analyse NGS data for population genetics purposes☆176Updated last year
- A variational framework for inferring population structure from SNP genotype data.☆142Updated 2 years ago
- phylogenetics tools for linux (and other mostly posix compliant) computers☆121Updated 8 months ago
- ☆83Updated 3 months ago
- Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model☆172Updated 2 years ago
- Software for painlessly estimating average nucleotide diversity within and between populations☆140Updated last month
- Tools test whether admixture occurred and more☆210Updated last year
- Program for analysing NGS data.☆242Updated 6 months ago
- A fully reproducible and state-of-the-art ancient DNA analysis pipeline☆180Updated last week
- Estimating Effective Migration Surfaces☆106Updated last year
- Efficient phylogenomic software by maximum likelihood☆202Updated 3 years ago
- Calculate summary statistics and manipulate multiple sequence alignments☆85Updated last year
- Infer a tree sequence from genetic variation data.☆60Updated last week
- mixture classification, constraint optimization, outlier detection, population structure, admixture history, and selection detection.☆87Updated 4 years ago
- Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction☆246Updated this week
- Lecture Notes on Computational and Mathematical Population Genetics☆191Updated 4 years ago
- Bayesian analysis of genomic sequence data under the multispecies coalescent model☆106Updated 3 weeks ago
- Inference of ploidy and heterozygosity structure using whole genome sequencing data☆277Updated 2 weeks ago
- A flexible, scalable, and reproducible pipeline to automate variant calling from raw sequence reads, with lots of bells and whistles - fo…☆106Updated 2 months ago
- A set of functions to visualise genotypes based on a VCF☆87Updated 3 years ago
- Population genetic simulations in R 🌍☆60Updated last month
- Recovering genes from targeted sequence capture data☆128Updated 2 months ago
- An imagemagick-like frontend to Biopython SeqIO☆116Updated last year
- Effective selection of population size projection for construction of the site frequency spectrum. Convert VCF to dadi/fastsimcoal style …☆156Updated last year
- A toolkit for analyzing and visualizing phylogenetic placement data☆62Updated 7 months ago
- Assembly and intrahost/low-frequency variant calling for viral samples☆143Updated last week
- Fast calculation of Patterson's D (ABBA-BABA) and the f4-ratio statistics across many populations/species☆177Updated 9 months ago