a UNIX shell toolkit for processing and analyzing multiple sequence alignments and phylogenies
☆82Mar 23, 2026Updated this week
Alternatives and similar repositories for PhyKIT
Users that are interested in PhyKIT are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference☆88Updated this week
- Bayesian gene tree reconciliation and WGD inference using amalgamated likelihood estimation☆16Apr 29, 2025Updated 11 months ago
- a broadly applicable tool for automated gene identification and retrieval☆41Updated this week
- a versatile toolkit for processing and analyzing diverse types of sequence data☆22Feb 18, 2026Updated last month
- ksrates is a tool to position whole-genome duplications relative to speciation events using substitution-rate-adjusted mixed paralog-orth…☆23Jan 21, 2026Updated 2 months ago
- DigitalOcean Gradient AI Platform • AdBuild production-ready AI agents using customizable tools or access multiple LLMs through a single endpoint. Create custom knowledge bases or connect external data.
- Support material for the "Comparative Genomics Laboratory" classes of the MSc in Biodiversity and Evolution at the University of Bologna.☆13Feb 27, 2026Updated last month
- Fast and accurate Phylogeny estimation with self-attention Networks☆42Apr 19, 2025Updated 11 months ago
- Correcting errors in noisy long reads using variation graphs☆51Nov 17, 2022Updated 3 years ago
- a tree splitting and pruning algorithm for retrieving single-copy orthologs from gene family trees☆29Feb 23, 2026Updated last month
- Accurate Species Tree EstimatoR: a family of optimation algorithms for species tree inference (including ASTRAL & CASTER)☆232Updated this week
- Earl Grey: A fully automated TE curation and annotation pipeline☆200Updated this week
- A tool to infer species tree and phylogenetic network from multilocus data☆32Jul 2, 2020Updated 5 years ago
- spruceup☆25Aug 15, 2025Updated 7 months ago
- Tools for analyzing trees☆13Apr 16, 2025Updated 11 months ago
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click and start building anything your business needs.
- A Python package for testing evolutionary hypotheses in genome-wide approaches.☆33Mar 5, 2021Updated 5 years ago
- 🪡Correct and scaffold assemblies using long reads☆57Mar 10, 2026Updated 2 weeks ago
- oxford dot plots☆169Feb 17, 2026Updated last month
- assembly evaluation tool☆35May 11, 2022Updated 3 years ago
- ☆237Jan 24, 2025Updated last year
- An Illumina PE genome contig assembler, can handle large (17Gbp) complex (hexaploid) genomes.☆45Nov 25, 2022Updated 3 years ago
- A tool to root phylogenies☆23Sep 5, 2024Updated last year
- Hapo-G is a tool that aims to improve the quality of genome assemblies by polishing the consensus with accurate reads.☆26Oct 24, 2025Updated 5 months ago
- Visualing species tree from ASTRAL with gene tree discordance☆28May 13, 2025Updated 10 months ago
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- ☆42Apr 2, 2024Updated last year
- PREQUAL: a pre-alignment quality filter for comparative sequence analyses☆33Jun 1, 2022Updated 3 years ago
- PoSeiDon: positive selection detection and recombination analysis pipeline☆39Sep 22, 2025Updated 6 months ago
- phylogenetics tools for linux (and other mostly posix compliant) computers☆123Jan 17, 2025Updated last year
- Improved Inference of Ortholog Groups using Hidden Markov Models☆38Sep 14, 2025Updated 6 months ago
- Efficient phylogenetic tree inference for massive taxonomic datasets☆142Apr 6, 2025Updated 11 months ago
- ☆134Aug 29, 2024Updated last year
- Tool to plot synteny and structural rearrangements between genomes☆343Apr 7, 2025Updated 11 months ago
- Accurate Species TRee ALgorithm☆275Apr 1, 2024Updated last year
- Wordpress hosting with auto-scaling on Cloudways • AdFully Managed hosting built for WordPress-powered businesses that need reliable, auto-scalable hosting. Cloudways SafeUpdates now available.
- A script that parses the OrthoFinder output and keeps only the orthogroups that meet specific criteria☆19Oct 14, 2020Updated 5 years ago
- k-mer similarity analysis pipeline☆22Nov 20, 2025Updated 4 months ago
- ☆45Oct 29, 2022Updated 3 years ago
- GALBA is a pipeline for fully automated prediction of protein coding gene structures with AUGUSTUS in novel eukaryotic genomes for the sc…☆148Jan 27, 2025Updated last year
- Metaphor: a general-purpose workflow for assembly and binning of metagenomes☆40Nov 14, 2025Updated 4 months ago
- ☆78Jun 2, 2025Updated 9 months ago
- Tutorials on phylogenetic and phylogenomic inference☆396Sep 13, 2023Updated 2 years ago