HyPhy 2.5.x (Maintenance Mode — bug fixes only). All active development has moved to HyPhy 3: https://github.com/veg/hyphy-3
☆275Oct 13, 2026Updated 2 weeks ago
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☆55Jan 5, 2026Updated 9 months ago
- PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. Please report only **techni…☆209Jan 29, 2026Updated 9 months ago
- TOGA (Tool to infer Orthologs from Genome Alignments): implements a novel paradigm to infer orthologous genes. TOGA integrates gene annot…☆212Nov 23, 2025Updated 11 months ago
- Version 5 of the CAFE phylogenetics software☆183Oct 23, 2026Updated last week
- Methods for finding associations between phenotypic and genomic differences between species using the Forward Genomics framework☆24Mar 26, 2026Updated 7 months ago
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting for WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Deploy in minutes on Cloudways by DigitalOcean.
- Convergence analysis using relative rate and correcting for phylogenetic relatedness☆12Apr 25, 2025Updated last year
- BITACORA: A Bioinformatics tool for gene family annotation☆58Dec 10, 2025Updated 10 months ago
- Phylogenetic orthology inference for comparative genomics☆877Jul 15, 2025Updated last year
- Analysis of convergence between organismal traits and DNA/protein sequences☆71Sep 17, 2026Updated last month
- Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction☆257Updated this week
- SyntenyFinder contains a collection of scripts for performing and visualizing macrosynteny analyses. It supports annotated chromosome-lev…☆35Jan 15, 2025Updated last year
- A tool for automated alignment trimming in large-scale phylogenetic analyses. Development version: 2.0☆273Updated this week
- RAxML Next Generation: faster, easier-to-use and more flexible☆483Updated this week
- FastOMA is a scalable software package to infer orthology relationship.☆104Oct 26, 2026Updated last week
- 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.
- PhyloAcc a software to detect the changes of conservation of a genomic region☆39Updated this week
- Estimating gene family turnover rates by likelihood-based methods☆12Aug 17, 2020Updated 6 years ago
- ☆352Mar 4, 2025Updated last year
- Another Gtf/Gff Analysis Toolkit https://nbisweden.github.io/AGAT/☆589Sep 7, 2026Updated last month
- Convergent substitution detection tool based on the PCOC model☆32Dec 2, 2021Updated 4 years ago
- HyPhy tutorials☆11Apr 9, 2018Updated 8 years ago
- ☆83May 2, 2026Updated 6 months ago
- Accurate Species Tree EstimatoR: a family of optimation algorithms for species tree inference (including ASTRAL & CASTER)☆262Jun 25, 2026Updated 4 months ago
- Scalable relaxed clock phylogenetic dating☆29Jul 5, 2026Updated 3 months ago
- Open source password manager - Proton Pass • AdSecurely store, share, and autofill your credentials with Proton Pass, the end-to-end encrypted password manager trusted by millions.
- Process, visualize, and analyze phylogenetic trees☆13Updated this week
- Automatically exported from code.google.com/p/prank-msa☆41Mar 19, 2026Updated 7 months ago
- Phylogenetics between and within hosts at once, all along the genome.☆51Oct 2, 2024Updated 2 years ago
- Official home of genome aligner based upon notion of Cactus graphs☆716Updated this week
- Synteny and Rearrangement Identifier☆496Jul 1, 2026Updated 4 months ago
- Analyzing combinations of codon substitution histories☆48Updated this week
- shell tools for processing phylogenetic trees☆120Aug 30, 2022Updated 4 years ago
- CAAStools is a bioinformatics toolbox that allows the user to identify and validate CAAS on MSA of orthologous proteins.☆26Nov 21, 2023Updated 2 years ago
- a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference☆96Oct 26, 2026Updated last week
- Bare Metal GPUs on DigitalOcean Gradient AI • AdPurpose-built for serious AI teams training foundational models, running large-scale inference, and pushing the boundaries of what's possible.
- An imagemagick-like frontend to Biopython SeqIO☆121Mar 18, 2024Updated 2 years ago
- Tools for improving the sensitivity and specificity of genome alignments☆58Mar 12, 2026Updated 7 months ago
- phylogenetics tools for linux (and other mostly posix compliant) computers☆127Apr 18, 2026Updated 6 months ago
- Pairwise whole genome aligner☆245Sep 4, 2026Updated last month
- GALBA is a pipeline for fully automated prediction of protein coding gene structures with AUGUSTUS in novel eukaryotic genomes for the sc…☆150Apr 13, 2026Updated 6 months ago
- ☆205Oct 5, 2026Updated 3 weeks ago
- Scripts used in the annotation of B10K genomes☆17Jun 1, 2020Updated 6 years ago