Python script calculating transposable element density for all genes in a genome. Publication: https://mobilednajournal.biomedcentral.com/articles/10.1186/s13100-022-00264-4
☆37Sep 30, 2024Updated last year
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:
- SINE annotation tool for plant genomes☆19Jan 21, 2024Updated 2 years ago
- Long-reads Gap-free Chromosome-scale Assembler☆79Mar 21, 2023Updated 3 years 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
- Whole Genome Annotation Pipeline☆16Jun 20, 2025Updated 11 months ago
- Computational Analysis of Gene Expression Evolution☆48Apr 17, 2026Updated 2 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.
- SyntenyFinder contains a collection of scripts for performing and visualizing macrosynteny analyses. It supports annotated chromosome-lev…☆35Jan 15, 2025Updated last year
- HELIANO is a software for detection and classification of Helitron-like elements.☆33Jun 10, 2025Updated last year
- ☆245Jan 24, 2025Updated last year
- TransposonUltimate - a holistic set of tools for transposon identification☆86Mar 4, 2022Updated 4 years ago
- Hybrid error correction approach for long reads using overlap graph☆11Sep 26, 2023Updated 2 years ago
- Study of TE evolution in a population of genomes☆10Dec 11, 2023Updated 2 years ago
- Neural network classification of TE☆100Apr 3, 2026Updated 2 months ago
- Detailed bioinformatics scripts and methods used in the NAM genome paper.☆92Jan 14, 2025Updated last year
- a tool to evaluate long-read error correction mainly with PacBio High-Fidelity Reads (HiFi reads).☆20Dec 5, 2023Updated 2 years ago
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- Nextflow pipeline for scaffolding genome assemblies with Hi-C reads☆16Nov 5, 2025Updated 7 months ago
- Easily construct the ML species tree with single-copy gene shared by different species.☆27Oct 26, 2018Updated 7 years ago
- ☆11Mar 14, 2026Updated 3 months 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
- ☆15Jan 19, 2022Updated 4 years ago
- A Python package for testing evolutionary hypotheses in genome-wide approaches.☆33Mar 5, 2021Updated 5 years ago
- TEsorter: an accurate and fast method to classify LTR-retrotransposons in plant genomes☆110Nov 17, 2025Updated 7 months ago
- 3DGB is a workflow to build 3D models of genomes from HiC data☆13May 6, 2026Updated last month
- A genome assembly assessment pipeline.☆38Jun 5, 2026Updated last week
- AI Agents on DigitalOcean Gradient AI Platform • AdBuild production-ready AI agents using customizable tools or access multiple LLMs through a single endpoint. Create custom knowledge bases or connect external data.
- read and analyse RepeatMasker output☆27May 22, 2023Updated 3 years ago
- A simple program for evaluate the assembly of a give genome.☆18Mar 3, 2023Updated 3 years ago
- 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
- Sensitive alignment of genomes with high sequence diversity, extensive structural polymorphism and whole-genome duplication variation☆194Oct 15, 2025Updated 8 months ago
- CAAStools is a bioinformatics toolbox that allows the user to identify and validate CAAS on MSA of orthologous proteins.☆23Nov 21, 2023Updated 2 years ago
- Methods and recipes for Plant Genome Annotation - Transposable Elements☆20Jun 10, 2025Updated last year
- Some useful gadgets☆12Mar 14, 2022Updated 4 years ago
- HiC-Hiker: A probabilistic model to determine contig orientation in chromosome-length scaffolds with Hi-C☆26Jan 14, 2021Updated 5 years ago
- An R package to visualize chromosome scale repeat patterns and predict centromere locations.☆47May 8, 2026Updated last month
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click. Zero configuration with optimized deployments.
- RepeatIdentifier☆74Mar 19, 2025Updated last year
- This pipeline is used to distinguish allotetraploid subgenomes.☆11Apr 8, 2024Updated 2 years ago
- ☆17Oct 21, 2024Updated last year
- ☆37Nov 30, 2023Updated 2 years ago
- A pipeline used to identify different modes of duplicated gene pairs☆120Jul 22, 2025Updated 10 months ago
- parallelLastz: Running Lastz in parallel☆18Sep 13, 2024Updated last year
- Decomposition Into Single-COpy gene trees (DISCO) is a method for decomposing multi-copy gene-family trees while attempting to preserve o…☆12Jun 19, 2025Updated last year