a UNIX shell toolkit for processing and analyzing multiple sequence alignments and phylogenies
☆89Jul 20, 2026Updated 3 weeks ago
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☆92Aug 6, 2026Updated last week
- Bayesian gene tree reconciliation and WGD inference using amalgamated likelihood estimation☆16Apr 29, 2025Updated last year
- a versatile toolkit for processing and analyzing diverse types of sequence data☆24May 19, 2026Updated 2 months ago
- a broadly applicable tool for automated gene identification and retrieval☆42Jun 16, 2026Updated 2 months ago
- ksrates is a tool to position whole-genome duplications relative to speciation events using substitution-rate-adjusted mixed paralog-orth…☆25Jul 20, 2026Updated 3 weeks ago
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- Correcting errors in noisy long reads using variation graphs☆53Nov 17, 2022Updated 3 years ago
- a tree splitting and pruning algorithm for retrieving single-copy orthologs from gene family trees☆32Jul 13, 2026Updated last month
- Accurate Species Tree EstimatoR: a family of optimation algorithms for species tree inference (including ASTRAL & CASTER)☆257Jun 25, 2026Updated last month
- Earl Grey: A fully automated TE curation and annotation pipeline☆221Aug 11, 2026Updated last week
- A tool to infer species tree and phylogenetic network from multilocus data☆32Jul 2, 2020Updated 6 years ago
- spruceup☆25Aug 15, 2025Updated last year
- Fast and accurate Phylogeny estimation with self-attention Networks☆42Apr 19, 2025Updated last year
- Tools for analyzing trees☆13Apr 16, 2025Updated last year
- oxford dot plots☆173Jul 2, 2026Updated last month
- 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.
- 🪡Correct and scaffold assemblies using long reads☆58Apr 1, 2026Updated 4 months ago
- An Illumina PE genome contig assembler, can handle large (17Gbp) complex (hexaploid) genomes.☆46Nov 25, 2022Updated 3 years ago
- A Python package for testing evolutionary hypotheses in genome-wide approaches.☆33Mar 5, 2021Updated 5 years ago
- assembly evaluation tool☆35May 11, 2022Updated 4 years ago
- ☆258Jan 24, 2025Updated last year
- A tool to root phylogenies☆23Sep 5, 2024Updated last year
- ☆43Apr 2, 2024Updated 2 years ago
- Hapo-G is a tool that aims to improve the quality of genome assemblies by polishing the consensus with accurate reads.☆26Oct 24, 2025Updated 9 months ago
- phylogenetics tools for linux (and other mostly posix compliant) computers☆127Apr 18, 2026Updated 4 months ago
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- PREQUAL: a pre-alignment quality filter for comparative sequence analyses☆34Jun 1, 2022Updated 4 years ago
- A script that parses the OrthoFinder output and keeps only the orthogroups that meet specific criteria☆19Oct 14, 2020Updated 5 years ago
- PoSeiDon: positive selection detection and recombination analysis pipeline☆40Sep 22, 2025Updated 10 months ago
- Inference of Ortholog Groups using Hidden Markov Models☆39May 12, 2026Updated 3 months ago
- Efficient phylogenetic tree inference for massive taxonomic datasets☆147Apr 6, 2025Updated last year
- Tool to plot synteny and structural rearrangements between genomes☆353Jul 27, 2026Updated 3 weeks ago
- Accurate Species TRee ALgorithm☆281Apr 1, 2024Updated 2 years ago
- ☆137Aug 29, 2024Updated last year
- Support material for the "Comparative Genomics Laboratory" classes of the MSc in Biodiversity and Evolution at the University of Bologna.☆13Feb 27, 2026Updated 5 months ago
- End-to-end encrypted email - Proton Mail • AdSpecial offer: 40% Off Yearly / 80% Off First Month. All Proton services are open source and independently audited for security.
- Code for TAD_SV project☆11Mar 16, 2022Updated 4 years ago
- HyPhy tutorials☆11Apr 9, 2018Updated 8 years ago
- Leviathan: A fast, memory-efficient, and scalable taxonomic and pathway profiler for (pan)genome-resolved metagenomics and metatranscript…☆26Aug 4, 2026Updated 2 weeks ago
- k-mer similarity analysis pipeline☆24Jul 27, 2026Updated 3 weeks ago
- tree visualization for tree + annotation data☆62Jun 17, 2025Updated last year
- ☆83May 2, 2026Updated 3 months ago
- GALBA is a pipeline for fully automated prediction of protein coding gene structures with AUGUSTUS in novel eukaryotic genomes for the sc…☆149Apr 13, 2026Updated 4 months ago