K-mer substring space decomposition

Pipelines for the production of Treeval data

Kmer-db is a fast and memory-efficient tool for large-scale k-mer analyses (indexing, querying, estimating evolutionary relationships, etc.).

Pipeline for homeobox gene identification

Find, circularise and annotate mitogenome from PacBio assemblies

A genome completeness evaluation tool based on miniprot

k-mer learning materials

Work for the tree sequence inference paper.

Sampling and manipulating genome-wide ancestral recombination graphs (ARGs)

A K-mer classifier for HiFi reads

FastK based version of Merqury

Contains the description of a file format to store kmers and associated values

Laplace transformed coalescence time distributions

Diagnostic index expectation maximisation (diem) algorithm implementations

Phase, partition and visualize subgenomes of a neoallopolyploid or hybrid based on the subgenome-specific repetitive kmers.

a tool for inferring species tree from sequencing reads

Assembled Genomes Compressor

Coalescent simulations for k-mer spectra

Repository for Edelman et al 2018

heterozygosity-based estimator of Rho - https://academic.oup.com/genetics/advance-article/doi/10.1093/genetics/iyac100/6623412

A fast K-mer counter for high-fidelity shotgun datasets

Alignment-based retrieval and concatenation of phylogenetic markers from whole genome sequence (WGS) data

A high-performance, Pythonic language for bioinformatics

Phylogenetic orthology inference for comparative genomics

A derivative of GenomeScope2.0 modified to work with FastK

Utilities to detect and profile `het-kmers`