HyPhy: Hypothesis testing using Phylogenies
☆255May 1, 2026Updated this week
Alternatives and similar repositories for hyphy
Users that are interested in hyphy are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- HyPhy standalone analyses☆53Jan 5, 2026Updated 3 months ago
- PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. Please report only **techni…☆192Jan 29, 2026Updated 3 months ago
- Methods for finding associations between phenotypic and genomic differences between species using the Forward Genomics framework☆24Mar 26, 2026Updated last month
- Version 5 of the CAFE phylogenetics software☆166Mar 16, 2026Updated last month
- Estimating gene family turnover rates by likelihood-based methods☆12Aug 17, 2020Updated 5 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.
- Phylogenetic orthology inference for comparative genomics☆854Jul 15, 2025Updated 9 months ago
- TOGA (Tool to infer Orthologs from Genome Alignments): implements a novel paradigm to infer orthologous genes. TOGA integrates gene annot…☆205Nov 23, 2025Updated 5 months ago
- HyPhy tutorials☆11Apr 9, 2018Updated 8 years ago
- BITACORA: A Bioinformatics tool for gene family annotation☆54Dec 10, 2025Updated 4 months ago
- SyntenyFinder contains a collection of scripts for performing and visualizing macrosynteny analyses. It supports annotated chromosome-lev…☆35Jan 15, 2025Updated last year
- Analysis of convergence between organismal traits and DNA/protein sequences☆65Apr 17, 2026Updated 2 weeks ago
- Newick tree processing☆13Mar 25, 2026Updated last month
- ☆78Jun 2, 2025Updated 11 months ago
- PhyloAcc a software to detect the changes of conservation of a genomic region☆35Apr 27, 2026Updated last week
- 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.
- Convergent substitution detection tool based on the PCOC model☆31Dec 2, 2021Updated 4 years ago
- A tool for automated alignment trimming in large-scale phylogenetic analyses. Development version: 2.0☆259Updated this week
- PhyloBayes: phylogenetic reconstruction using infinite mixtures (CAT and CAT-GTR) -- serial version (for MPI, see pbmpi.git)☆15Oct 21, 2021Updated 4 years ago
- Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction☆251Updated this week
- Accurate Species Tree EstimatoR: a family of optimation algorithms for species tree inference (including ASTRAL & CASTER)☆241Updated this week
- a UNIX shell toolkit for processing and analyzing multiple sequence alignments and phylogenies☆84Apr 19, 2026Updated 2 weeks ago
- Gene tree - species tree reconciliation from gene tree distributions☆39Apr 28, 2026Updated last week
- Analyzing combinations of codon substitution histories☆46Apr 7, 2026Updated 3 weeks ago
- Genome wide orthology inference and dNdS estimation☆101Mar 25, 2026Updated last month
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- Python HyPhy: Facilitating HyPhy execution and parsing☆21Dec 7, 2021Updated 4 years ago
- ☆348Mar 4, 2025Updated last year
- RAxML Next Generation: faster, easier-to-use and more flexible☆463Apr 27, 2026Updated last week
- Scalable relaxed clock phylogenetic dating☆28Sep 3, 2025Updated 8 months ago
- Clann: Investigation of phylogenomic signal using supertrees☆18Apr 21, 2026Updated last week
- Another Gtf/Gff Analysis Toolkit https://nbisweden.github.io/AGAT/☆570Apr 13, 2026Updated 3 weeks ago
- Killifish genomics scripts☆12Feb 19, 2021Updated 5 years ago
- Scripts used in the annotation of B10K genomes☆15Jun 1, 2020Updated 5 years ago
- An imagemagick-like frontend to Biopython SeqIO☆117Mar 18, 2024Updated 2 years ago
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- shell tools for processing phylogenetic trees☆119Aug 30, 2022Updated 3 years ago
- Best-fit model selection☆89Mar 21, 2024Updated 2 years ago
- Tools for improving the sensitivity and specificity of genome alignments☆58Mar 12, 2026Updated last month
- phylogenetics tools for linux (and other mostly posix compliant) computers☆123Apr 18, 2026Updated 2 weeks ago
- Reconstruction of ancestral genome maps☆16Mar 29, 2018Updated 8 years ago
- FastOMA is a scalable software package to infer orthology relationship.☆97Apr 24, 2026Updated last week
- A genome completeness evaluation tool based on miniprot☆239Sep 18, 2025Updated 7 months ago