Analyze changes in gene family size and provide a statistical foundation for evolutionary inferences.
☆119Apr 7, 2021Updated 4 years ago
Alternatives and similar repositories for CAFE
Users that are interested in CAFE are comparing it to the libraries listed below
Sorting:
- Version 5 of the CAFE phylogenetics software☆163Feb 12, 2025Updated last year
- A tool to extract and visualize the results of CAFE (Computational Analysis of gene Family Evolution)☆63Sep 5, 2019Updated 6 years ago
- PASA software☆199Feb 12, 2025Updated last year
- LTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also…☆214Mar 9, 2026Updated last week
- Python package and CLI for whole-genome duplication related analyses. **This package is deprecated in favor of** https://github.com/heche…☆86Jan 6, 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…☆451Oct 20, 2025Updated 5 months ago
- iTAK☆48May 22, 2024Updated last year
- OrthoFiller: Identifying missing annotations for evolutionarily conserved genes.☆22Dec 1, 2022Updated 3 years ago
- ☆12Nov 23, 2020Updated 5 years ago
- A pipeline used to identify different modes of duplicated gene pairs☆119Jul 22, 2025Updated 7 months ago
- Phylogenetic orthology inference for comparative genomics☆839Jul 15, 2025Updated 8 months ago
- Python library to facilitate genome assembly, annotation, and comparative genomics☆892Mar 12, 2026Updated last week
- FASconCAT-G offers a wide range of possibilities to edit and concatenate multiple nucleotide, amino acid, and structure sequence alignmen…☆35Jun 12, 2024Updated last year
- Scripts used in the annotation of B10K genomes☆15Jun 1, 2020Updated 5 years ago
- Extensive de-novo TE Annotator☆435Mar 12, 2026Updated last week
- Ultra-fast de novo assembler using long noisy reads☆136Feb 24, 2021Updated 5 years ago
- Mummer alignment tool☆551Feb 4, 2025Updated last year
- 3D de novo assembly (3D DNA) pipeline☆223Nov 29, 2023Updated 2 years ago
- ALLHiC: phasing and scaffolding polyploid genomes based on Hi-C data☆179Oct 20, 2024Updated last year
- ☆29Jul 16, 2022Updated 3 years ago
- Gene prediction software☆67Oct 22, 2022Updated 3 years ago
- Taxon-aware analysis of clustered protein sequences☆31Jul 1, 2024Updated last year
- Automates running of OrthoMCL software from http://orthomcl.org/common/downloads/software/v2.0/☆80Jul 31, 2020Updated 5 years ago
- Genome Scripts used in fungal comparative genomics☆65Sep 25, 2020Updated 5 years ago
- Calculate circos format data of GC content and GC skew from genome data.☆12Sep 20, 2025Updated 6 months ago
- Synteny and Rearrangement Identifier☆453Mar 13, 2026Updated last week
- NOVOPlasty - The organelle assembler and heteroplasmy caller☆198Feb 4, 2024Updated 2 years ago
- Inference of ploidy and heterozygosity structure using whole genome sequencing data☆292Feb 25, 2026Updated 3 weeks ago
- Code to perform homolog detectability analyses as described in Weisman et al. 2020 (https://www.biorxiv.org/content/10.1101/2020.02.27.96…☆18Nov 18, 2024Updated last year
- a tool to identify species and inter-species hybrids and chromosome copy number variants from short-read data☆19Sep 13, 2019Updated 6 years ago
- Fast and accurately polish the genome generated by long reads.☆240Jan 9, 2025Updated last year
- PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. Please report only **techni…☆185Jan 29, 2026Updated last month
- Fast and pretty dotplots for whole genomes assemblies using minimap and R/ggplot2☆77Aug 30, 2016Updated 9 years ago
- Guided synteny alignment between duplicated genomes (within specified quota constraint)☆59Sep 5, 2017Updated 8 years ago
- EasyCodeML: A visual tool for analysis of selection using CodeML☆83May 7, 2023Updated 2 years ago
- Fast genome analysis from unassembled short reads☆317Apr 8, 2024Updated last year
- ☆64Mar 14, 2024Updated 2 years ago
- dnaPipeTE (for de-novo assembly & annotation Pipeline for Transposable Elements), is a pipeline designed to find, annotate and quantify T…☆60Mar 29, 2023Updated 2 years ago
- Genome annotation with AUGUSTUS☆328Aug 15, 2025Updated 7 months ago