Workflow for Building Microsynteny Networks
☆61Jul 30, 2022Updated 3 years ago
Alternatives and similar repositories for SynNet-Pipeline
Users that are interested in SynNet-Pipeline are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Synteny matrix representation with maximum likelihood pipeline☆16Jul 7, 2021Updated 5 years ago
- An R package to infer and analyze synteny networks from protein sequences☆43Jul 23, 2025Updated last year
- MCScanX: Multiple Collinearity Scan toolkit X version. The most popular synteny analysis tool in the world!☆293Oct 4, 2025Updated 9 months ago
- The code used in the manuscript titled "Gene duplication and evolution in recurring polyploidization-diploidization cycles in plants".☆29Mar 19, 2021Updated 5 years ago
- Gennome annotation scripts for the crickets Gryllus bimaculatus and Laupala kohalensis.☆14Feb 28, 2022Updated 4 years ago
- 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.
- A shiny application to visualize MCscan result☆37Jun 26, 2026Updated last month
- A Python package for testing evolutionary hypotheses in genome-wide approaches.☆33Mar 5, 2021Updated 5 years ago
- methods for orphan gene prediction paper optimization☆25Dec 24, 2021Updated 4 years ago
- ☆25Nov 29, 2022Updated 3 years ago
- Pipeline for Phylostratigraphy☆13Nov 2, 2022Updated 3 years ago
- Long-reads Gap-free Chromosome-scale Assembler☆79Mar 21, 2023Updated 3 years ago
- SynVisio is an interactive multiscale visualization tool that lets you explore the results of McScanX a popular synteny and collinearity …☆94Updated this week
- TOGA (Tool to infer Orthologs from Genome Alignments): implements a novel paradigm to infer orthologous genes. TOGA integrates gene annot…☆209Nov 23, 2025Updated 8 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 6 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.
- A quick user guide for de novo transposable element (TE) library generation and TE screening. Utilising; the Extensive de novo TE Annotat…☆27Dec 7, 2022Updated 3 years ago
- A pipeline used to identify different modes of duplicated gene pairs☆121Jul 22, 2025Updated last year
- A box of genomics tools☆22Jun 10, 2026Updated last month
- This is code for running Orthofinder -> PAML☆13Jul 27, 2016Updated 10 years ago
- Codes for the lettuce resequencing project in 2020☆31Jun 28, 2021Updated 5 years ago
- Instruction and scripts for reconstructing ancestral genome from pairwise syntenic blocks using MLGO☆13Oct 30, 2018Updated 7 years ago
- Genome alignment and synteny plots☆36Mar 24, 2026Updated 4 months ago
- CNEFinder: Finding Conserved Non-coding Elements in Genomes☆25Jul 21, 2021Updated 5 years ago
- ☆13Oct 30, 2019Updated 6 years ago
- GPU virtual machines on DigitalOcean Gradient AI • AdGet to production fast with high-performance AMD and NVIDIA GPUs you can spin up in seconds. The definition of operational simplicity.
- Mikado is a lightweight Python3 pipeline whose purpose is to facilitate the identification of expressed loci from RNA-Seq data * and to s…☆112Jan 30, 2026Updated 5 months ago
- Genome wide orthology inference and dNdS estimation☆100Jun 30, 2026Updated 3 weeks ago
- From the comparison of two extant genomes and corresponding gene families, PhylDiag detects conserved segments, i.e. segments of chromoso…☆15Aug 7, 2023Updated 2 years ago
- A personal pipeline to calculate Ka,Ks and Ka/Ks using PAML-yn00 with YN method☆10Feb 26, 2025Updated last year
- Strand and WGD aware syntenic gene identification☆16Oct 16, 2025Updated 9 months ago
- A pipeline to use Lep-Map3 to create linkage maps and LepAnchor for anchoring and orienting genome assemblies with said linkage maps.☆15Jun 24, 2025Updated last year
- ☆17Nov 19, 2025Updated 8 months ago
- Scripts to do haplotype analysis on pan genomes.☆20Sep 24, 2020Updated 5 years ago
- Pipeline for homeobox gene identification☆11Aug 8, 2023Updated 2 years ago
- 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.
- ☆13Nov 15, 2017Updated 8 years ago
- An R package to identify and classify duplicated genes from whole-genome protein sequence data☆36Sep 11, 2025Updated 10 months ago
- Python library to facilitate genome assembly, annotation, and comparative genomics☆925Jul 20, 2026Updated last week
- The GitHub repository for the A. thaliana pan-NLR'ome project.☆18Jun 6, 2019Updated 7 years ago
- Tool set for processing fasta/fastq/table formated data. Usually they are perl scripts.☆56Jul 15, 2026Updated 2 weeks ago
- SCORPiOs is a synteny-guided gene tree correction pipeline for clades that have undergone a whole-genome duplication event.☆24Sep 23, 2024Updated last year
- Phylogenetic iDentification of Subgenomes☆10Jul 7, 2022Updated 4 years ago