Scripts to analyze data using TreeMix. This pipeline runs TreeMix with bootstrapping, helps choose number of migration events and creates a consensus tree. It plots the maximum likelihood tree with bootstrap values, drift and residuals and calculates statistics for every migration event, such as migration support, standard error and p-values.
☆47Mar 7, 2024Updated 2 years ago
Alternatives and similar repositories for TreeMix
Users that are interested in TreeMix are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Fast calculation of Patterson's D (ABBA-BABA) and the f4-ratio statistics across many populations/species☆186Dec 19, 2024Updated last year
- Heuristic search algorithm for fitting qpGraph models☆11Aug 4, 2022Updated 3 years ago
- Tutorial on using popular tools for learning about population history☆54Jul 18, 2018Updated 7 years ago
- Topology weighting by iterative sampling of sub-trees☆87Jan 5, 2025Updated last year
- This repository contains the code and manual for the R package delimitR.☆17Apr 19, 2022Updated 4 years ago
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- Inferring natural selection by comparative population genomic analysis across species☆27Oct 31, 2023Updated 2 years ago
- R package for analysis of hybrids and hybrid zones☆21Dec 30, 2023Updated 2 years ago
- A collection of tools useful for preparing or manipulating site-frequency spectrum (SFS) files☆21Mar 20, 2023Updated 3 years ago
- MSMC2 Scripts☆28Sep 24, 2025Updated 7 months ago
- ☆19Jan 24, 2018Updated 8 years ago
- R functions for generating site frequency spectra (SFS) from a VCF file.☆29Feb 13, 2020Updated 6 years ago
- ☆24Mar 15, 2026Updated last month
- This is a tool for speculation of ancestral allel, calculation of sfs and drawing its bar plot. It is easy-to-use and runing fast. What y…☆11Dec 16, 2022Updated 3 years ago
- ☆16Jan 6, 2022Updated 4 years ago
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- ☆24Jun 9, 2017Updated 8 years ago
- Bayesian analysis of genomic sequence data under the multispecies coalescent model☆113Apr 14, 2026Updated 2 weeks ago
- ☆11Dec 1, 2020Updated 5 years ago
- Tools for F1 hybrid PSMC (hPSMC) divergence time inference from whole genomes☆15May 29, 2024Updated last year
- Tutorials on phylogenomic analyses for the ForBio Phylogenomics course☆41Mar 4, 2024Updated 2 years ago
- ☆68Dec 5, 2022Updated 3 years ago
- Tutorials on phylogenetic and phylogenomic inference☆51May 4, 2025Updated 11 months ago
- Scripts and resources for the haploblocks manuscript☆18Mar 20, 2020Updated 6 years ago
- Genome-wide scan for balancing selection using beta statistic☆32Apr 26, 2023Updated 3 years ago
- GPU virtual machines on DigitalOcean Gradient AI • AdGet to production fast with high-performance AMD and NVIDIA GPUs you can spin up in seconds. The definition of operational simplicity.
- Quantifying Introgression via Branch Lengths☆57Sep 30, 2022Updated 3 years ago
- A tool for estimating time-dependent migration rates based on cross-/within-population coalescent rates from MSMC☆16Apr 6, 2025Updated last year
- A new simple and efficient software to PCA and Cluster For popolation VCF File☆83Jun 25, 2025Updated 10 months ago
- Snakemake workflow for highly parallel variant calling designed for ease-of-use in non-model organisms.☆89Apr 13, 2026Updated 2 weeks ago
- ☆38Apr 13, 2026Updated 2 weeks ago
- ☆95Jun 7, 2025Updated 10 months ago
- An R function to compute Concordance Factors from SNP datasets☆15Dec 4, 2025Updated 4 months ago
- An R Package to build and simulate coalescent models☆20Apr 22, 2026Updated last week
- SMC++ infers population history from whole-genome sequence data.☆173Jan 20, 2024Updated 2 years ago
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- SambaR: Snp datA Management and Basic Analyses in R☆32Oct 16, 2025Updated 6 months ago
- an ensemble usage of MAFFT-linsi --add on large datasets☆13May 31, 2024Updated last year
- Accurate Species Tree EstimatoR: a family of optimation algorithms for species tree inference (including ASTRAL & CASTER)☆241Updated this week
- Scripts for analysis used during the course☆96Apr 30, 2024Updated 2 years ago
- ☆24Mar 17, 2026Updated last month
- Effective selection of population size projection for construction of the site frequency spectrum. Convert VCF to dadi/fastsimcoal style …☆173Apr 17, 2026Updated last week
- Automated pipeline for running CoalHMM☆13Jan 9, 2026Updated 3 months ago