Python script calculating transposable element density for all genes in a genome. Publication: https://mobilednajournal.biomedcentral.com/articles/10.1186/s13100-022-00264-4
☆38Oct 26, 2026Updated last week
Alternatives and similar repositories for TE_Density
Users that are interested in TE_Density are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- ☆15Jan 19, 2022Updated 4 years ago
- Long-reads Gap-free Chromosome-scale Assembler☆79Mar 21, 2023Updated 3 years ago
- Study of TE evolution in a population of genomes☆12Dec 11, 2023Updated 2 years ago
- A Python package for testing evolutionary hypotheses in genome-wide approaches.☆33Mar 5, 2021Updated 5 years ago
- ☆37Nov 30, 2023Updated 2 years ago
- Simple, predictable pricing with DigitalOcean hosting • AdAlways know what you'll pay with monthly caps and flat pricing. Enterprise-grade infrastructure trusted by 600k+ customers.
- Hybrid error correction approach for long reads using overlap graph☆11Sep 26, 2023Updated 3 years ago
- SINE annotation tool for plant genomes☆19Jan 21, 2024Updated 2 years ago
- Neural network classification of TE☆104Apr 3, 2026Updated 7 months ago
- Scripts for Wang et al (2020) Evidence for widespread selection in shaping the genomic landscape during speciation of Populus.☆11Feb 15, 2020Updated 6 years ago
- ☆271Jan 24, 2025Updated last year
- Phylogenomic species tree inference under gene duplication and loss☆13Sep 20, 2026Updated last month
- ☆11Oct 23, 2024Updated 2 years ago
- This repository contains relevant code and explanation for ”Leveraging a phased pangenome to design ideal haplotypes for hybrid potato br…☆41Oct 17, 2026Updated 2 weeks ago
- Easily construct the ML species tree with single-copy gene shared by different species.☆27Oct 26, 2018Updated 8 years ago
- Proton VPN Special Offer - Get 70% off • AdSpecial partner offer. Trusted by over 100 million users worldwide. Tested, Approved and Recommended by Experts.
- HiC-Hiker: A probabilistic model to determine contig orientation in chromosome-length scaffolds with Hi-C☆26Jan 14, 2021Updated 5 years ago
- HELIANO is a software for detection and classification of Helitron-like elements.☆35Jul 13, 2026Updated 3 months ago
- SyntenyFinder contains a collection of scripts for performing and visualizing macrosynteny analyses. It supports annotated chromosome-lev…☆35Jan 15, 2025Updated last year
- read and analyse RepeatMasker output☆26May 22, 2023Updated 3 years ago
- Earl Grey: A fully automated TE curation and annotation pipeline☆227Oct 28, 2026Updated last week
- Convert RepeatMasker ".out" file into a gff3 with colors!!!☆27Aug 20, 2020Updated 6 years ago
- A genome assembly assessment pipeline.☆39Jun 5, 2026Updated 5 months ago
- Robust identification of orthologous Synteny with the Orthology Index☆43Updated this week
- Methods and recipes for Plant Genome Annotation - Transposable Elements☆21Jun 10, 2025Updated last year
- Serverless GPU API endpoints on Runpod - Get Bonus Credits • AdSkip the infrastructure headaches. Auto-scaling, pay-as-you-go, no-ops approach lets you focus on innovating your application.
- TOGA (Tool to infer Orthologs from Genome Alignments): implements a novel paradigm to infer orthologous genes. TOGA integrates gene annot…☆212Nov 23, 2025Updated 11 months ago
- Sensitive alignment of genomes with high sequence diversity, extensive structural polymorphism and whole-genome duplication variation☆203Aug 17, 2026Updated 2 months ago
- Module and script to remove contamination in assembled genomes before submission to ncbi☆14Jul 28, 2025Updated last year
- Tree-based orthology inference with functionality for reducing contamination☆11May 22, 2026Updated 5 months ago
- A pipeline used to identify different modes of duplicated gene pairs☆127Jul 22, 2025Updated last year
- RepeatIdentifier☆76Mar 19, 2025Updated last year
- Nextflow pipeline for scaffolding genome assemblies with Hi-C reads☆16Nov 5, 2025Updated last year
- An Example of Subgenome Phasing for Complex Allopolyploidy☆17Nov 6, 2025Updated last year
- a fork of the gap-closing pipeline PBJelly☆15Jan 7, 2019Updated 7 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.
- Algorithm For Gene Order Reconstruction in Ancestors☆87Jul 8, 2026Updated 3 months ago
- TransposonUltimate - a holistic set of tools for transposon identification☆86Mar 4, 2022Updated 4 years ago
- This is a modified version of EviAnn -- zgtools☆10Updated this week
- We developed GenomeSyn as a new tool for constructing and visualizing genome synteny, its novel design and implementation can serve as a …☆36Jan 3, 2022Updated 4 years ago
- Scripts for Shi et al. (2024). The suer-pangenome of Populus unveils genomic facets for its adaptation and diversification in widespread …☆20Apr 1, 2024Updated 2 years ago
- Detailed bioinformatics scripts and methods used in the NAM genome paper.☆97Jan 14, 2025Updated last year
- ☆12Jun 12, 2023Updated 3 years ago