A tool for plotting CAFE5 gene family expansion/contraction result

MCScanX: Multiple Collinearity Scan toolkit X version. The most popular synteny analysis tool in the world!

HAST: Haplotype-Resolved Assembly for Synthetic Long Reads Using A Trio-Binning Strategy

assembly evaluation tool

Centromics: visualing centromeres with multiple omics data

Generate an interactive dot plot from mummer or minimap alignments

Calculate

Hierarchical Alignment Format

shell tools for processing phylogenetic trees

TAD calling, phase imputation, 3D modeling and more for diploid single-cell Hi-C (Dip-C) and general Hi-C

Reference-based variant calling pipeline for a pair of phased haplotype assemblies

Find, circularise and annotate mitogenome from PacBio assemblies

Tool for assessing/improving assembly quality in extra-long tandem repeats

NCBI C++ Toolkit package sources

An algorithm for centromere assembly using long error-prone reads

A Hi-C scaffolding method

Yet another Hi-C scaffolding tool

Software to assemble contigs/scaffolds into chromosomes using Hi-C data

A tool to infer species tree and phylogenetic network from multilocus data

Small general purpose library for C and Python with focus on bioinformatics.

Automatic DNA methylation detection from nanopore tools and their consensus model

A computation framework for genome-wide detection of enhancer-hijacking events from chromatin interaction data in re-arranged genomes

Tools to find TE-gene chimera

MapOptics is a lightweight cross-platform tool that enables the user to visualise and interact with the alignment of Bionano optical mapping data and can be used for in depth exploration of hybrid …

Chimericognizer is a novel and accurate chimeric contigs correction tool based on optical maps.