Donovan H. Parks

CompareM. A toolbox for comparative genomics.

STAMP. Statistical Analysis of Metagenomic Profiles

RefineM. A toolbox for improving metagenome-assembled genomes.

Background-Subtraction-Library. C++ background substraction library

PhyloRank. Assign taxonomic ranks based on evolutionary divergence.

UniteM. Ensemble binning strategies for combining the output of multiple binning methods.

biolib. Python package for common tasks in bioinformatic.

GenomeTreeTk. A toolbox for working with genome trees.

ExpressBetaDiversity. Taxon- and phylogenetic-based beta diversity measures.

pygmy. Visualization of large trees and associated metadata

FragmentClassificationPackage. Homology- and composition-based classifiers for assigning a taxonomic attribution to metagenomic fragments.

CommunityM. Identify, classify, and assemble 16S reads in metagenomic data.

GeneTreeTk. A toolbox for working with gene trees.

ANI-Cache. Cache-aware ANI calculations.

khill. K-HILL calculates the effective number of genomes in a collection of assembled genomes.

SketchM. Fast genome ANI estimation using k-mer sketches.

DBB. Bin scaffolds from a single metagenomic sample into population genomes.

DBSCAN. Clustering of sequences from environmental samples.

PETs. Putative Evolutionary Trees