Phylogenetic orthology inference for comparative genomics
☆846Jul 15, 2025Updated 8 months ago
Alternatives and similar repositories for OrthoFinder
Users that are interested in OrthoFinder are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Python library to facilitate genome assembly, annotation, and comparative genomics☆899Apr 2, 2026Updated last week
- Mummer alignment tool☆554Feb 4, 2025Updated last year
- BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET/EP/ETP and AUGUSTUS in novel eu…☆455Apr 7, 2026Updated last week
- MCScanX: Multiple Collinearity Scan toolkit X version. The most popular synteny analysis tool in the world!☆281Oct 4, 2025Updated 6 months ago
- Extensive de-novo TE Annotator☆439Apr 5, 2026Updated last week
- Virtual machines for every use case on DigitalOcean • AdGet dependable uptime with 99.99% SLA, simple security tools, and predictable monthly pricing with DigitalOcean's virtual machines, called Droplets.
- PASA software☆199Feb 12, 2025Updated last year
- Fast genome-wide functional annotation through orthology assignment☆722Mar 24, 2026Updated 3 weeks ago
- Genome annotation with AUGUSTUS☆330Aug 15, 2025Updated 8 months ago
- Another Gtf/Gff Analysis Toolkit https://nbisweden.github.io/AGAT/☆568Jan 13, 2026Updated 3 months ago
- Accelerated BLAST compatible local sequence aligner.☆1,278Mar 28, 2026Updated 2 weeks ago
- Synteny and Rearrangement Identifier☆460Mar 17, 2026Updated 3 weeks ago
- TransDecoder source☆304Mar 22, 2026Updated 3 weeks ago
- Version 5 of the CAFE phylogenetics software☆165Mar 16, 2026Updated 3 weeks ago
- Eukaryotic Genome Annotation Pipeline☆385Apr 8, 2026Updated last week
- AI Agents on 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.
- An accurate GFF3/GTF lift over pipeline☆532Aug 1, 2023Updated 2 years ago
- Official home of genome aligner based upon notion of Cactus graphs☆671Apr 3, 2026Updated last week
- Analyze changes in gene family size and provide a statistical foundation for evolutionary inferences.☆119Apr 7, 2021Updated 5 years ago
- Accurate Species TRee ALgorithm☆277Apr 1, 2024Updated 2 years ago
- GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more☆471Updated this week
- Fast genome analysis from unassembled short reads☆318Apr 8, 2024Updated 2 years ago
- Tools for fast and flexible genome assembly scaffolding and improvement☆563Feb 14, 2024Updated 2 years ago
- Hifiasm: a haplotype-resolved assembler for accurate Hifi reads☆764Mar 18, 2025Updated last year
- ☆237Jan 24, 2025Updated last year
- Wordpress hosting with auto-scaling - Free Trial • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- De-Novo Repeat Discovery Tool☆235Jul 21, 2025Updated 8 months ago
- Align proteins to genomes with splicing and frameshift☆398Jan 5, 2026Updated 3 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 4 months ago
- ALLHiC: phasing and scaffolding polyploid genomes based on Hi-C data☆179Oct 20, 2024Updated last year
- HyPhy: Hypothesis testing using Phylogenies☆254Mar 23, 2026Updated 3 weeks ago
- Genome-scale protein function classification☆375Updated this week
- Organelle Genome Assembly Toolkit (Chloroplast/Mitocondrial/ITS)☆375Feb 13, 2025Updated last year
- Pilon is an automated genome assembly improvement and variant detection tool☆380Apr 10, 2022Updated 4 years ago
- A pipeline used to identify different modes of duplicated gene pairs☆120Jul 22, 2025Updated 8 months ago
- Serverless GPU API endpoints on Runpod - Bonus Credits • AdSkip the infrastructure headaches. Auto-scaling, pay-as-you-go, no-ops approach lets you focus on innovating your application.
- A versatile pairwise aligner for genomic and spliced nucleotide sequences☆2,154Updated this week
- Trinity RNA-Seq de novo transcriptome assembly☆887Feb 7, 2025Updated last year
- MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics☆204Aug 25, 2025Updated 7 months ago
- A tool for automated alignment trimming in large-scale phylogenetic analyses. Development version: 2.0☆255Updated this week
- A genome completeness evaluation tool based on miniprot☆238Sep 18, 2025Updated 6 months ago
- A cross-platform and ultrafast toolkit for FASTA/Q file manipulation☆1,537Mar 31, 2026Updated 2 weeks ago
- Program for aligning DNA sequences, a pairwise aligner.☆243Mar 27, 2026Updated 2 weeks ago