apetkau / orthomcl-pipelineView external linksLinks
Automates running of OrthoMCL software from http://orthomcl.org/common/downloads/software/v2.0/
☆80Jul 31, 2020Updated 5 years ago
Alternatives and similar repositories for orthomcl-pipeline
Users that are interested in orthomcl-pipeline are comparing it to the libraries listed below
Sorting:
- Microbial Whole Genome Sequence data analysis labs for 2014☆29Jul 31, 2020Updated 5 years ago
- Creates Venn diagrams for OrthoMCL output☆17Aug 9, 2017Updated 8 years ago
- scripts and intermediate files used to annotate TEs in Jiao et al.☆34Apr 12, 2018Updated 7 years ago
- A tool to extract and visualize the results of CAFE (Computational Analysis of gene Family Evolution)☆63Sep 5, 2019Updated 6 years ago
- ☆14Jul 27, 2019Updated 6 years ago
- Analyze changes in gene family size and provide a statistical foundation for evolutionary inferences.☆119Apr 7, 2021Updated 4 years ago
- A powerful Perl module for simulating the genome digestions by restriction enzymes☆14Sep 10, 2024Updated last year
- Guided synteny alignment between duplicated genomes (within specified quota constraint)☆59Sep 5, 2017Updated 8 years ago
- Python library to facilitate genome assembly, annotation, and comparative genomics☆889Dec 22, 2025Updated last month
- Pan-genome wide association studies☆207May 29, 2024Updated last year
- ☆25Mar 22, 2016Updated 9 years ago
- My collection of light bioinformatics analysis pipelines for specific tasks☆79May 20, 2024Updated last year
- Generate an interactive dot plot from mummer or minimap alignments☆211Jan 17, 2024Updated 2 years ago
- Easily construct the ML species tree with single-copy gene shared by different species.☆27Oct 26, 2018Updated 7 years ago
- Compare different genome alignment tools using a wide range of genomes with different complexities.☆14Dec 3, 2022Updated 3 years ago
- LTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also…☆215Jun 25, 2025Updated 7 months ago
- Wrapper script to concatenate, align, and construct phylogenetic trees of BUSCOs☆20Sep 18, 2019Updated 6 years ago
- Plastid Genome Annotator☆54Oct 29, 2020Updated 5 years ago
- Ultra-fast de novo assembler using long noisy reads☆136Feb 24, 2021Updated 4 years ago
- Genome Scripts used in fungal comparative genomics☆65Sep 25, 2020Updated 5 years ago
- Scripts to do haplotype analysis on pan genomes.☆20Sep 24, 2020Updated 5 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
- A tool to filter BUSCO output into single-copy gene files for phylogenomics☆13Jul 24, 2024Updated last year
- Phylogenetic orthology inference for comparative genomics☆829Jul 15, 2025Updated 7 months ago
- Automatically exported from code.google.com/p/prottest3☆37Jan 22, 2018Updated 8 years ago
- scripts to parse and analyse MCScanX collinearity output☆32Mar 3, 2020Updated 5 years ago
- Parallel implementation of OrthoMCL☆21Aug 26, 2022Updated 3 years ago
- Fast genome-wide functional annotation through orthology assignment☆700Jun 18, 2025Updated 7 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 last month
- Modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets☆209Aug 21, 2024Updated last year
- ☆14Mar 13, 2018Updated 7 years ago
- Interactive, web tool for exploring pan-genome of bacterial strains☆49Jan 14, 2026Updated last month
- Tool set for processing fasta/fastq/table formated data. Usually they are perl scripts.☆56Updated this week
- ☆73Jun 2, 2023Updated 2 years ago
- ☆17Nov 19, 2025Updated 2 months ago
- 🗻 Visualization of genome/gene sequence synteny☆42Dec 13, 2023Updated 2 years ago
- Version 5 of the CAFE phylogenetics software☆159Feb 12, 2025Updated last year
- Genome-scale protein function classification☆367Updated this week
- This python script can be used to detect Whole-genome duplication (WGD) with the dS based method.☆25Feb 22, 2019Updated 6 years ago