Guided synteny alignment between duplicated genomes (within specified quota constraint)
☆59Sep 5, 2017Updated 8 years ago
Alternatives and similar repositories for quota-alignment
Users that are interested in quota-alignment are comparing it to the libraries listed below
Sorting:
- Fast and pretty dotplots for whole genomes assemblies using minimap and R/ggplot2☆77Aug 30, 2016Updated 9 years ago
- A tool to analyze synteny at the protein level.☆14Mar 28, 2018Updated 7 years ago
- OrthoFiller: Identifying missing annotations for evolutionarily conserved genes.☆22Dec 1, 2022Updated 3 years ago
- A tool for recovering synteny blocks from multiple alignment☆32Oct 18, 2021Updated 4 years ago
- ☆13Nov 15, 2017Updated 8 years ago
- Everything but the kitchen sink☆12Feb 6, 2025Updated last year
- Unzip assembly graphs with Hi-C data and/or long reads.☆27Sep 20, 2024Updated last year
- Same species annotation lift over pipeline.☆97Jul 21, 2023Updated 2 years ago
- A program to generate a graph which presents a simplified representation of several full length genomes☆13Aug 23, 2018Updated 7 years ago
- defusion☆14Aug 24, 2021Updated 4 years ago
- A set of scripts to help automate the construction of data sets for multi-gene phylogenetic analyses.☆13Mar 13, 2019Updated 6 years ago
- profile the repeat landscape in a genome☆16Sep 9, 2014Updated 11 years ago
- Synteny Imager☆65Dec 18, 2025Updated 2 months ago
- BESST - scaffolder for genomic assemblies☆58Jul 6, 2023Updated 2 years ago
- My collection of light bioinformatics analysis pipelines for specific tasks☆79May 20, 2024Updated last year
- Identification of conserved non-coding sequences in plants☆32Feb 4, 2026Updated last month
- A comparative genome scaffolding tool☆16Oct 6, 2018Updated 7 years ago
- PanEffect is a JavaScript framework to explore variant effects across a pangenome. The tool has two views that allows a user to (1) expl…☆13Jan 30, 2024Updated 2 years ago
- ☆28Dec 1, 2022Updated 3 years ago
- Improved Phased Assembler☆28Mar 11, 2022Updated 3 years ago
- An Illumina PE genome contig assembler, can handle large (17Gbp) complex (hexaploid) genomes.☆45Nov 25, 2022Updated 3 years ago
- Neural network classification of TE☆97Oct 9, 2025Updated 4 months ago
- base-level dotplots from PAF alignments☆32Sep 18, 2025Updated 5 months ago
- Dot: An interactive dot plot viewer for comparative genomics☆35May 4, 2023Updated 2 years ago
- scripts to parse and analyse MCScanX collinearity output☆32Mar 3, 2020Updated 6 years ago
- scripts and intermediate files used to annotate TEs in Jiao et al.☆34Apr 12, 2018Updated 7 years ago
- a precise pangenome browser combining linear and graph-based pan-genome☆13Jul 16, 2024Updated last year
- Modeling gene duplication, loss, and coalescence (through parsimony)☆10Jun 18, 2020Updated 5 years ago
- Scaffolding of genomic assemblies with RNA seq data☆15Oct 8, 2015Updated 10 years ago
- Identifying large scale inversions between two genomes by mapping genome 1's unique kmers onto genome 2.☆10Jun 6, 2025Updated 9 months ago
- A couple of tools I find indispensable for post orthomcl down-stream analysis.☆11Oct 2, 2019Updated 6 years ago
- de novo targeted gene assembly☆22Apr 16, 2021Updated 4 years ago
- Peregrine: Fast Genome Assembler Using SHIMMER Index☆102Feb 6, 2022Updated 4 years ago
- Integrated toolkit for analysis and evaluation of annotated genomes☆25Aug 1, 2025Updated 7 months ago
- Modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets☆211Aug 21, 2024Updated last year
- Simple tools for working with Hi-C data☆18Dec 19, 2018Updated 7 years ago
- Command-line program to wrap dagchainer and combine pairwise results into multi-alignments in column format☆21Oct 15, 2010Updated 15 years ago
- Online material and code base for the article Coordinates and Intervals in Graph Based Reference Genomes☆11May 2, 2017Updated 8 years ago
- Modified TIR-Learner for Rice genome☆12Jun 14, 2019Updated 6 years ago