A tool to extract and visualize the results of CAFE (Computational Analysis of gene Family Evolution)
☆65Sep 5, 2019Updated 7 years ago
Alternatives and similar repositories for CAFE_fig
Users that are interested in CAFE_fig are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- showTree can visualize the phylogeny, protein sequences and protein domains of a gene family in one figure.☆31Mar 28, 2019Updated 7 years ago
- Straightforward & minimalistic removal of poorly aligned regions in sequence alignments.☆17Mar 18, 2019Updated 7 years ago
- A tool for plotting CAFE5 gene family expansion/contraction result☆37Sep 22, 2023Updated 3 years ago
- Version 5 of the CAFE phylogenetics software☆179Mar 16, 2026Updated 6 months ago
- Analyze changes in gene family size and provide a statistical foundation for evolutionary inferences.☆127Apr 7, 2021Updated 5 years ago
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click. Zero configuration with optimized deployments.
- A pipeline used to identify different modes of duplicated gene pairs☆123Jul 22, 2025Updated last year
- ksrates is a tool to position whole-genome duplications relative to speciation events using substitution-rate-adjusted mixed paralog-orth…☆25Sep 18, 2026Updated last week
- WGDI: A user-friendly toolkit for evolutionary analyses of whole-genome duplications and ancestral karyotypes☆174Nov 4, 2025Updated 10 months ago
- Scripts used in the annotation of B10K genomes☆16Jun 1, 2020Updated 6 years ago
- Automates running of OrthoMCL software from http://orthomcl.org/common/downloads/software/v2.0/☆79Jul 31, 2020Updated 6 years ago
- A pipeline to identify gene family using mutiple tools and scripts.☆12Aug 22, 2021Updated 5 years ago
- issues for semina "Data Visulization"☆13Dec 23, 2025Updated 9 months ago
- Python package and CLI for whole-genome duplication related analyses. **This package is deprecated in favor of** https://github.com/heche…☆86Jan 6, 2026Updated 8 months ago
- Genome annotation with AUGUSTUS☆342May 30, 2026Updated 3 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.
- Perl script for manipulating multiple sequence alignments for phylogenetic reconstruction☆11Sep 29, 2014Updated 11 years ago
- Algorithm For Gene Order Reconstruction in Ancestors☆86Jul 8, 2026Updated 2 months ago
- Synteny and Rearrangement Identifier☆491Jul 1, 2026Updated 2 months ago
- BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET/EP/ETP and AUGUSTUS in novel eu…☆467Jun 17, 2026Updated 3 months ago
- ALLHiC: phasing and scaffolding polyploid genomes based on Hi-C data☆180Oct 20, 2024Updated last year
- Centromics: visualing centromeres with multiple omics data☆28Mar 4, 2025Updated last year
- MCScanX: Multiple Collinearity Scan toolkit X version. The most popular synteny analysis tool in the world!☆297Oct 4, 2025Updated 11 months ago
- PlantTribes is a collection of automated gene family analysis pipelines for comparative plant genomics☆38Apr 28, 2023Updated 3 years ago
- MitoZ: A toolkit for assembly, annotation, and visualization of animal mitochondrial genomes☆150Nov 6, 2024Updated last year
- 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.
- Find, circularise and annotate mitogenome from PacBio assemblies☆202May 11, 2025Updated last year
- ☆26Dec 15, 2025Updated 9 months ago
- ☆20Apr 24, 2022Updated 4 years ago
- Extensive de-novo TE Annotator☆469Sep 10, 2026Updated 2 weeks ago
- Codes for Vmap1.1 and Vmap3☆11Jan 5, 2026Updated 8 months ago
- A Plant Presence/absence Variants Scanner and Pan-genome Construction Pipeline☆27May 24, 2021Updated 5 years ago
- ☆33Apr 7, 2025Updated last year
- To phase, partition and visualize subgenomes of a neoallopolyploid or hybrid based on the subgenome-specific repetitive kmers.☆76Jun 4, 2026Updated 3 months ago
- ☆77Apr 23, 2020Updated 6 years ago
- 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.
- Fast calculation of Patterson's D (ABBA-BABA) and the f4-ratio statistics across many populations/species☆191Dec 19, 2024Updated last year
- Python library to facilitate genome assembly, annotation, and comparative genomics☆931Sep 19, 2026Updated last week
- A collection of scripts for working with Hi-C data, Juicebox, and other genomic file formats☆70May 22, 2021Updated 5 years ago
- Easily construct the ML species tree with single-copy gene shared by different species.☆27Oct 26, 2018Updated 7 years ago
- Resources for the Col-CEN reference genome assemblies☆12Feb 15, 2022Updated 4 years ago
- Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model☆195Nov 17, 2025Updated 10 months ago
- Generate an interactive dot plot from mummer or minimap alignments☆220Jan 17, 2024Updated 2 years ago