Softwares
Repeat-Aware $k$-mer-based Mutation Rate Estimators
A repeat-aware $k$-mer-based mutation rate estimator that published in [WABI 2025](https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2025.20), which needs the abundance histograms of $k$-mers in the reference genome.
This is the publication repository of our WABI 2025 paper.
This tool estimates substitution rate based on k-spectrum
This is an improved implementation of the estimator by leveraging KMC and sourmash.
This repository builds upon the ideas from https://github.com/medvedevgroup/Repeat-Aware_Substitution_Rate_Estimator/, with significant optimizations and extensions. It enables fast computation of mutation rates (genomic distances) between two whole genomes, leveraging KMC and sourmash.
We extend the estimator to construct Neighbor-Joining (NJ) tree among multiple genomes in parallel.
This tool efficiently estimates phylogenetic distances among multiple reference or assembly genomes in parallel. It is based on https://github.com/medvedevgroup/Repeat-Aware_Substitution_Rate_Estimator and https://github.com/Wu-Haonan/Repeat-Aware_mutation_rate_estimator, leveraging the power of KMC for k-mer counting and sourmash for sketching.
Repeat-Robust $k$-mer-based Mutation Rate Estimators
A repeat-robust $k$-mer-based mutation rate estimator that published in [ISMB 2026](https://www.biorxiv.org/content/10.64898/2026.04.01.715966v1.full)
This is the publication repository of our ISMB 2026 paper.
Repeat-aware estimator of mutation rate under whole/sub-sequence mutation mode
This is an improved implementation of the estimator as a sourmash plugin.
An improved version of https://github.com/medvedevgroup/Accurate_repeat-aware_kmer_based_estimator
Protein-Protein Interaction Sites Prediction
A structural-based predicting protein-protein interaction sites using the graph neural network. Our tool Spatom is also hosted on the webserver (http://118.190.151.48/Spatom/server)