A toolkit for identifying recombination and recombinant genotypes
☆26Dec 3, 2025Updated 2 months ago
Alternatives and similar repositories for HaplotypeTools
Users that are interested in HaplotypeTools are comparing it to the libraries listed below
Sorting:
- This tool performs an automatic identification, annotation, and analysis of the MYB gene family in plants. It can be applied to new trans…☆20Oct 12, 2025Updated 4 months ago
- ☆11Feb 4, 2026Updated 3 weeks ago
- Homologizer: phasing gene copies into polyploid subgenomes☆11Feb 3, 2026Updated 3 weeks ago
- Decomposition Into Single-COpy gene trees (DISCO) is a method for decomposing multi-copy gene-family trees while attempting to preserve o…☆11Jun 19, 2025Updated 8 months ago
- Ploidy agnostic phasing pipeline and algorithm☆49Jan 3, 2024Updated 2 years ago
- ☆12Jun 12, 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
- Full GATK SNP calling pipeline☆24Oct 30, 2025Updated 4 months ago
- Synteny matrix representation with maximum likelihood pipeline☆16Jul 7, 2021Updated 4 years ago
- ☆21Dec 8, 2025Updated 2 months ago
- A software package for local ancestry inference and haplotype phasing☆45Apr 20, 2023Updated 2 years ago
- De novo chromosome-level scaffolding and phasing tool using Hi-C☆30Nov 23, 2025Updated 3 months ago
- Genome assembly scaffolding using information from paired-end/mate-pair libraries, long reads, and synteny to closely related species.☆24Dec 6, 2018Updated 7 years ago
- A genome annotation pipeline that use short and long sequencing reads alignments from animal genomes☆30Apr 10, 2024Updated last year
- Efficient Local Ancestry Inference☆17Nov 10, 2025Updated 3 months ago
- CATG (Collinearity-based Assembly correcTor GUI) is a tool that can correct genome assembly with collinearity and generate tour files for…☆17Jan 24, 2026Updated last month
- Software package for estimating fine-scale recombination rate.☆17Jun 8, 2021Updated 4 years ago
- Phasing reads with secondary alignments☆22Nov 30, 2024Updated last year
- ☆37Feb 22, 2023Updated 3 years ago
- The repository serves as a public and official hosting of the pSONIC program (Conover et al., 2021).☆21Sep 9, 2021Updated 4 years ago
- The MafFilter genome alignment processor☆19Jan 6, 2026Updated last month
- BUSCOMP: BUSCO Compiler and Comparison tool☆21Sep 19, 2024Updated last year
- R package for analysis of hybrids and hybrid zones☆21Dec 30, 2023Updated 2 years ago
- 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 3 weeks ago
- Dynamic Elongation of a Genome Assembly Path☆25Dec 15, 2025Updated 2 months ago
- MODAS: Multi-Omics Data Association Study toolkit☆21Nov 21, 2024Updated last year
- Minimizer-based assembly scaffolding and mapping using long reads☆47Feb 4, 2026Updated 3 weeks ago
- ksrates is a tool to position whole-genome duplications relative to speciation events using substitution-rate-adjusted mixed paralog-orth…☆21Jan 21, 2026Updated last month
- Scripts to do haplotype analysis on pan genomes.☆20Sep 24, 2020Updated 5 years ago
- Gapless provides combined scaffolding, gap-closing and assembly correction with long reads☆38Mar 5, 2023Updated 2 years ago
- Strand and WGD aware syntenic gene identification☆15Oct 16, 2025Updated 4 months ago
- misFinder: Identify mis-assemblies in an unbiased manner using reference and paired-end reads☆10Oct 17, 2015Updated 10 years ago
- Chromosome Scale Assembler: A high-throughput chromosome scale genome assembly pipeline for vertebrate genomes☆10Oct 16, 2024Updated last year
- A genome assembly assessment pipeline.☆37Nov 20, 2023Updated 2 years ago
- CGM 主站☆11Mar 10, 2025Updated 11 months ago
- This pipeline is used to distinguish allotetraploid subgenomes.☆11Apr 8, 2024Updated last year
- PhyloForge: Unifying micro and macro evolution with comprehensive genomic signals☆10May 17, 2024Updated last year
- Calculates the probability of a haplotype given a population reference panel☆12Dec 9, 2024Updated last year
- ☆26Mar 23, 2024Updated last year