emmanuelparadis / apeView external linksLinks
Analysis of Phylogenetics and Evolution
☆73Feb 3, 2026Updated last week
Alternatives and similar repositories for ape
Users that are interested in ape are comparing it to the libraries listed below
Sorting:
- Population and Evolutionary Genetics Analysis System☆29Dec 4, 2025Updated 2 months ago
- Bayesian Phylogenetic Inference Using Graphical Models and an Interactive Model-Specification Language☆79Updated this week
- Leaping through tree space: continuous phylogenetic inference for rooted and unrooted trees☆12Sep 6, 2023Updated 2 years ago
- ☆228Jan 28, 2026Updated 2 weeks ago
- Phylogenetic profiling with orthology data☆13Oct 10, 2025Updated 4 months ago
- ☆11Feb 9, 2025Updated last year
- Phylogenetic inference using Stan☆23Mar 6, 2025Updated 11 months ago
- An R package for comparative transcriptomic analyses of hybrids and their progenitors☆15Sep 5, 2024Updated last year
- babette is an R package to work with BEAST2☆46Dec 20, 2025Updated last month
- Base Classes and Functions for Phylogenetic Tree Input and Output☆103Nov 1, 2025Updated 3 months ago
- R package to calculate the similarity of two trees based on the number of shared four-taxon subtrees (or splits)☆16Feb 4, 2026Updated last week
- Explore spaces of phylogenetic trees☆29Aug 28, 2025Updated 5 months ago
- R We There Yet?☆32Mar 27, 2025Updated 10 months ago
- Semantic Similarity in Bio-Ontologies☆18Jan 30, 2026Updated 2 weeks ago
- ☆16Feb 20, 2024Updated last year
- Efficient phylogenetic tree inference for massive taxonomic datasets☆141Apr 6, 2025Updated 10 months ago
- Bayesian Evolutionary Analysis by Sampling Trees☆267Jan 22, 2026Updated 3 weeks ago
- Pipeline to detect PAVs (presence/absence variations) in genome comparison using whole genome alignment.☆29Mar 5, 2018Updated 7 years ago
- Racmacs R package for performing antigenic cartography☆24Jun 27, 2024Updated last year
- Biogeographic regionalization and spatial conservation☆19Jul 14, 2025Updated 6 months ago
- Tutorial on Bayesian phylogenetic analysis☆52Sep 21, 2017Updated 8 years ago
- A tool for automated alignment trimming in large-scale phylogenetic analyses. Development version: 2.0☆248Updated this week
- A versatile simulation engine for stochastic population dynamics models.☆23Nov 11, 2022Updated 3 years ago
- ☆19Jan 21, 2026Updated 3 weeks ago
- The MafFilter genome alignment processor☆19Jan 6, 2026Updated last month
- download files in R using wget -c☆16Aug 20, 2025Updated 5 months ago
- Phylogenetic maximum representation sampling: choosing most representative strains or taxa☆40Sep 23, 2025Updated 4 months ago
- a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference☆83Oct 17, 2025Updated 3 months ago
- Phylogenetic analysis in R☆214Updated this week
- ☆20Nov 18, 2021Updated 4 years ago
- general purpose library for evaluating the likelihood of sequence evolution on trees☆143Jan 30, 2026Updated 2 weeks ago
- A Python library that exposes features from IQ-TREE - efficient software for phylogenomic inference☆41Updated this week
- Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction☆249Updated this week
- Scripts to do haplotype analysis on pan genomes.☆20Sep 24, 2020Updated 5 years ago
- Utilities and distributions for (birth-death) skyline models.☆10Aug 27, 2019Updated 6 years ago
- Accurate Species Tree EstimatoR: a family of optimation algorithms for species tree inference (including ASTRAL & CASTER)☆225Jan 4, 2026Updated last month
- Protein hint generation pipeline for gene finding in eukaryotic genomes☆60Oct 27, 2023Updated 2 years ago
- spruceup☆25Aug 15, 2025Updated 5 months ago
- Scripts that used in our chicken T2T manuscript.☆22Jan 14, 2026Updated 3 weeks ago