LKremer / CAFE_figView external linksLinks
A tool to extract and visualize the results of CAFE (Computational Analysis of gene Family Evolution)
☆63Sep 5, 2019Updated 6 years ago
Alternatives and similar repositories for CAFE_fig
Users that are interested in CAFE_fig are comparing it to the libraries listed below
Sorting:
- showTree can visualize the phylogeny, protein sequences and protein domains of a gene family in one figure.☆31Mar 28, 2019Updated 6 years ago
- Straightforward & minimalistic removal of poorly aligned regions in sequence alignments.☆17Mar 18, 2019Updated 6 years ago
- A tool for plotting CAFE5 gene family expansion/contraction result☆36Sep 22, 2023Updated 2 years ago
- Version 5 of the CAFE phylogenetics software☆159Feb 12, 2025Updated last year
- Analyze changes in gene family size and provide a statistical foundation for evolutionary inferences.☆119Apr 7, 2021Updated 4 years ago
- A pipeline used to identify different modes of duplicated gene pairs☆117Jul 22, 2025Updated 6 months ago
- WGDI: A user-friendly toolkit for evolutionary analyses of whole-genome duplications and ancestral karyotypes☆159Nov 4, 2025Updated 3 months ago
- Automates running of OrthoMCL software from http://orthomcl.org/common/downloads/software/v2.0/☆80Jul 31, 2020Updated 5 years ago
- ksrates is a tool to position whole-genome duplications relative to speciation events using substitution-rate-adjusted mixed paralog-orth…☆20Jan 21, 2026Updated 3 weeks 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 last month
- Long read QC, assembly and scaffolding pipeline☆13Jul 13, 2020Updated 5 years ago
- Scripts used in the annotation of B10K genomes☆15Jun 1, 2020Updated 5 years ago
- To phase, partition and visualize subgenomes of a neoallopolyploid or hybrid based on the subgenome-specific repetitive kmers.☆70Mar 23, 2025Updated 10 months ago
- MitoZ: A toolkit for assembly, annotation, and visualization of animal mitochondrial genomes☆135Nov 6, 2024Updated 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…☆445Oct 20, 2025Updated 3 months ago
- Bayesian gene tree reconciliation and WGD inference using amalgamated likelihood estimation☆16Apr 29, 2025Updated 9 months ago
- Genome annotation with AUGUSTUS☆328Aug 15, 2025Updated 5 months ago
- Find, circularise and annotate mitogenome from PacBio assemblies☆191May 11, 2025Updated 9 months ago
- MCScanX: Multiple Collinearity Scan toolkit X version. The most popular synteny analysis tool in the world!☆276Oct 4, 2025Updated 4 months ago
- A Plant Presence/absence Variants Scanner and Pan-genome Construction Pipeline☆28May 24, 2021Updated 4 years ago
- ☆21Dec 30, 2025Updated last month
- Bayesian molecular clock dating tutorial with genome-scale datasets☆19Dec 4, 2021Updated 4 years ago
- ☆24Dec 15, 2025Updated last month
- Extensive de-novo TE Annotator☆429Oct 12, 2025Updated 4 months ago
- ☆76Apr 23, 2020Updated 5 years ago
- Easily construct the ML species tree with single-copy gene shared by different species.☆27Oct 26, 2018Updated 7 years ago
- Algorithm For Gene Order Reconstruction in Ancestors☆80Aug 16, 2025Updated 5 months ago
- Synteny and Rearrangement Identifier☆447Apr 29, 2025Updated 9 months ago
- Perl script for manipulating multiple sequence alignments for phylogenetic reconstruction☆11Sep 29, 2014Updated 11 years ago
- Fast calculation of Patterson's D (ABBA-BABA) and the f4-ratio statistics across many populations/species☆183Dec 19, 2024Updated last year
- A pipeline to identify gene family using mutiple tools and scripts.☆11Aug 22, 2021Updated 4 years ago
- 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
- ☆31Apr 7, 2025Updated 10 months ago
- ☆19Apr 24, 2022Updated 3 years ago
- The code used in the manuscript titled "Gene duplication and evolution in recurring polyploidization-diploidization cycles in plants".☆29Mar 19, 2021Updated 4 years ago
- Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model☆183Nov 17, 2025Updated 2 months ago
- A collection of scripts for working with Hi-C data, Juicebox, and other genomic file formats☆69May 22, 2021Updated 4 years ago
- Wrapper script to concatenate, align, and construct phylogenetic trees of BUSCOs☆20Sep 18, 2019Updated 6 years ago
- ALLHiC: phasing and scaffolding polyploid genomes based on Hi-C data☆177Oct 20, 2024Updated last year