base-level dotplots from PAF alignments

Foldseek enables fast and sensitive comparisons of large structure sets.

Python implementation of barrnap (Bacterial ribosomal RNA predictor)

🔬 ♌ Bacterial ribosomal RNA predictor

RAxML Next Generation: faster, easier-to-use and more flexible

PartitionFinder discovers optimal partitioning schemes for DNA sequences.

ChIP-seq peak-calling, QC and differential analysis pipeline.

a fork of the gap-closing pipeline PBJelly

tree visualization for tree + annotation data

Generate an interactive dot plot from mummer or minimap alignments

Close assembly gaps using long-reads at high accuracy.

Robust identification of orthologous Synteny with the Orthology Index

Example for evlutionary analyses with Orthology Index

A package for the extension of repetitive DNA sequences

Tools to process and analyze deep sequencing data.

Synteny and Rearrangement Identifier

Structural Variant Identification Method using Genome Assemblies

T2Tools is a toolset contains several tools for T2T assembly, and it is under development.

k-mer based assembly evaluation

A bioinformatics tool for working with modified bases

Python script calculating transposable element density for all genes in a genome. Publication: https://mobilednajournal.biomedcentral.com/articles/10.1186/s13100-022-00264-4

The second version of the Kraken taxonomic sequence classification system

perl cworld module and collection of utility/analysis scripts for C data (3C, 4C, 5C, Hi-C)

genome-level speciation simulation to recreate Ks curves

haplotypic duplication identification tool