An R package to identify and classify duplicated genes from whole-genome protein sequence data
☆32Sep 11, 2025Updated 5 months ago
Alternatives and similar repositories for doubletrouble
Users that are interested in doubletrouble are comparing it to the libraries listed below
Sorting:
- Diamond2GO is a set of tools that can rapidly assign Gene Ontology (GO) terms and perform functional enrichment for large-scale functiona…☆26Feb 4, 2026Updated last month
- TransposonPSI involves a PSI-blast search of a protein or nucleotide sequence against a set of profiles of proteins corresponding to majo…☆14Apr 28, 2020Updated 5 years ago
- Centromics: visualing centromeres with multiple omics data☆25Mar 4, 2025Updated last year
- wgd v2: a suite of tools to uncover and date ancient polyploidy and whole-genome duplication☆37Feb 12, 2025Updated last year
- a tree splitting and pruning algorithm for retrieving single-copy orthologs from gene family trees☆29Feb 23, 2026Updated last week
- The complete sequence of a Chinese individual☆11Oct 8, 2024Updated last year
- Pipeline for homeobox gene identification☆11Aug 8, 2023Updated 2 years ago
- Figures for the CHM13 T2T SD paper.☆10Sep 12, 2021Updated 4 years ago
- Fast long-read mapper and whole-genome aligner (accelerated version of minimap2)☆43Jan 7, 2026Updated 2 months ago
- This is the standalone version of the EviAnn pipeline☆140Feb 5, 2026Updated last month
- A set of bioconda packages for transposon annotations. During my masterthesis I downloaded lots of these tools and I want to make it easi…☆14Mar 4, 2022Updated 4 years ago
- an ensemble usage of MAFFT-linsi --add on large datasets☆13May 31, 2024Updated last year
- An R package to visualize chromosome scale repeat patterns and predict centromere locations.☆45Nov 1, 2025Updated 4 months ago
- Improved Inference of Ortholog Groups using Hidden Markov Models☆38Sep 14, 2025Updated 5 months ago
- Toolkit for Population Genetic Statistics from Pool-Sequenced Samples, e.g., in Evolve and Resequence experiments☆48Oct 15, 2025Updated 4 months ago
- Portable solution to generate genome alignment chains using lastz☆60Dec 20, 2025Updated 2 months ago
- A genome assembly assessment pipeline.☆37Nov 20, 2023Updated 2 years ago
- Software GMATA for SSR mining, marker designing, genotyping, plot etc.☆17Oct 6, 2025Updated 5 months ago
- Genome alignment and synteny plots☆33Jun 5, 2023Updated 2 years ago
- Identify short variants and structural variants from raw sequencing data or genomic sequences☆34Mar 27, 2024Updated last year
- ☆14Feb 18, 2026Updated 2 weeks ago
- Whole Genome Alignment Tools☆216Nov 6, 2025Updated 4 months ago
- Detecting IBD within low coverage ancient DNA data. Development Repository for software package that contains code for manuscript.☆14Jan 28, 2026Updated last month
- A gap-closing software tool that uses long reads to enhance genome assembly.☆23Apr 25, 2024Updated last year
- Script to help assessing the evolutionary history of a TE family☆16Sep 5, 2019Updated 6 years ago
- A tool for quick and accurate calculation of syntenic diversity.☆42Sep 22, 2025Updated 5 months ago
- Multi-genome synteny block visualization tool☆55Updated this week
- 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 tool for the recovery of unassembled telomeres from soft-clipped read alignments.☆50Feb 9, 2026Updated last month
- A snakemake workflow for de novo genome assembly. It produces chromosome-scale primary/phased assemblies complete with organelles (mitoch…☆33May 14, 2025Updated 9 months ago
- genEra is a fast and easy-to-use command-line tool that estimates the age of the last common ancestor of protein-coding gene families.☆53Nov 29, 2024Updated last year
- TOGA (Tool to infer Orthologs from Genome Alignments): implements a novel paradigm to infer orthologous genes. TOGA integrates gene annot…☆204Nov 23, 2025Updated 3 months ago
- LTR_Finder is an efficient program for finding full-length LTR retrotranspsons in genome sequences.☆51Jan 16, 2024Updated 2 years ago
- A fast tool for detecting and decomposing segmental duplications in genome assemblies☆55Jul 19, 2025Updated 7 months ago
- Efficient retrieval, download, and unification of genomic data from leading biodiversity databases☆18Updated this week
- Remove CCS reads with remnant PacBio adapter sequences and convert outputs to a compressed .fastq (.fastq.gz).☆104Jul 23, 2024Updated last year
- ☆29Updated this week
- ☆147Nov 5, 2025Updated 4 months ago
- SyntenyFinder contains a collection of scripts for performing and visualizing macrosynteny analyses. It supports annotated chromosome-lev…☆35Jan 15, 2025Updated last year