LTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also included in this package.
☆215Mar 3, 2026Updated this week
Alternatives and similar repositories for LTR_retriever
Users that are interested in LTR_retriever are comparing it to the libraries listed below
Sorting:
- Extensive de-novo TE Annotator☆430Updated this week
- A parallel wrapper for LTR_FINDER☆55Mar 23, 2025Updated 11 months ago
- ALLHiC: phasing and scaffolding polyploid genomes based on Hi-C data☆178Oct 20, 2024Updated last year
- LTR_Finder is an efficient program for finding full-length LTR retrotranspsons in genome sequences.☆51Jan 16, 2024Updated 2 years ago
- TEsorter: an accurate and fast method to classify LTR-retrotransposons in plant genomes☆106Nov 17, 2025Updated 3 months ago
- haplotypic duplication identification tool☆275Oct 30, 2025Updated 4 months ago
- Synteny and Rearrangement Identifier☆448Apr 29, 2025Updated 10 months ago
- A gap-closing software tool that uses long reads to enhance genome assembly.☆233Sep 6, 2024Updated last year
- Python library to facilitate genome assembly, annotation, and comparative genomics☆890Updated this week
- De-Novo Repeat Discovery Tool☆231Jul 21, 2025Updated 7 months ago
- A telomere-to-telomere toolkit for gap-free genome assembly and centromeric repeat identification☆167Oct 29, 2025Updated 4 months ago
- Tools for fast and flexible genome assembly scaffolding and improvement☆559Feb 14, 2024Updated 2 years ago
- Fast and accurately polish the genome generated by long reads.☆240Jan 9, 2025Updated last year
- k-mer based assembly evaluation☆339Jun 28, 2024Updated last year
- Inference of ploidy and heterozygosity structure using whole genome sequencing data☆292Feb 25, 2026Updated last week
- PASA software☆197Feb 12, 2025Updated last year
- Fast and accurate de novo assembler for long reads☆398May 10, 2024Updated last year
- 3D de novo assembly (3D DNA) pipeline☆222Nov 29, 2023Updated 2 years ago
- BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET/EP/ETP and AUGUSTUS in novel eu…☆449Oct 20, 2025Updated 4 months ago
- To phase, partition and visualize subgenomes of a neoallopolyploid or hybrid based on the subgenome-specific repetitive kmers.☆70Mar 23, 2025Updated 11 months ago
- use long sequenced reads to close gaps in assemblies☆41Sep 4, 2018Updated 7 years ago
- Hifiasm: a haplotype-resolved assembler for accurate Hifi reads☆743Mar 18, 2025Updated 11 months ago
- Fast genome analysis from unassembled short reads☆313Apr 8, 2024Updated last year
- A genomic k-mer counter (and sequence utility) with nice features.☆160Jul 4, 2025Updated 8 months ago
- MCScanX: Multiple Collinearity Scan toolkit X version. The most popular synteny analysis tool in the world!☆277Oct 4, 2025Updated 5 months ago
- Redundans is a pipeline that assists an assembly of heterozygous/polymorphic genomes.☆173Apr 14, 2025Updated 10 months ago
- WGDI: A user-friendly toolkit for evolutionary analyses of whole-genome duplications and ancestral karyotypes☆159Nov 4, 2025Updated 4 months ago
- Generate an interactive dot plot from mummer or minimap alignments☆212Jan 17, 2024Updated 2 years ago
- Analyze changes in gene family size and provide a statistical foundation for evolutionary inferences.☆119Apr 7, 2021Updated 4 years ago
- Create a pseudohaploid assembly from a partially resolved diploid assembly☆32Nov 22, 2019Updated 6 years ago
- source code for EVM☆122Nov 29, 2024Updated last year
- Python package and CLI for whole-genome duplication related analyses. **This package is deprecated in favor of** https://github.com/heche…☆86Jan 6, 2026Updated 2 months ago
- Any Way to Show Multi genomic Synteny☆218Jul 4, 2025Updated 8 months ago
- Yet another k-mer analyzer☆161Dec 30, 2025Updated 2 months ago
- A genome completeness evaluation tool based on miniprot☆235Sep 18, 2025Updated 5 months ago
- A simple and fast metassembler and assembly gap filler designed for long molecule based assemblies.☆207Nov 18, 2022Updated 3 years ago
- RaGOO is no longer supported. Please use RagTag instead: https://github.com/malonge/RagTag☆173May 30, 2021Updated 4 years ago
- A pipeline used to identify different modes of duplicated gene pairs☆119Jul 22, 2025Updated 7 months ago
- Version 5 of the CAFE phylogenetics software☆161Feb 12, 2025Updated last year