SIMMER: prediction of microbiome enzymes that metabolize drugs and dietary compounds

Maast: discovery and genotyping of genetic variants in large numbers of genomes or sequencing reads

EukDetect: marker gene based detection of microbial eukaryotes in shotgun metagenomes

gt-pro: k-mer based metagenotyping of microbiome species from shotgun metagenomes with code that runs on a laptop

MIDAS and MIDAS2: Metagenomic Intra-species Diversity Analysis System for quantifying strain-level copy number and single nucleotide variation in shotgun metagenomes

Phylogenize: Phylogenetic regression to associate genes with traits estimated from metagenomic data

PhylOTU: Phylogenetic clustering of metagenomic sequences into operational taxonomic units (OTUs)

MicrobeCensus: Average genome size estimation from shotgun data

ShotMap: Tools for classifying shotgun metagenomic reads into protein families

MetaQuery: Annotation and quantitative analysis of genes in the human microbiome

MetaPASSAGE: A Metagenomic Pipeline for Automated Simulations and Analysis of Gene Families

Genome Structure

Contact map scoring: Methods for scoring differences in two chromatin interaction maps

Akita: Deep-learning model of 3D genome folding from sequence alone

ShapeMF: Gibbs sampling algorithm for de novo discovery of DNA shape motifs

TargetFinder: Enhancer-promoter 3D interaction models

Regulatory Genomics

CellWalkR: integrative modeling of single-cell and bulk data via random walks on a network

G-NEST: a gene neighborhood scoring tool to identify co-expressed, co-conserved genes


Comparative & Population Genomics

AcceleratedRegionsNF: Next-flow pipeline for identifying accelerated regions in multiple sequence alignments.

AlleleAnalyzer: Genetic variation-aware CRISPR gRNA design tool

PHAST package (with Adam Siepel, Melissa Hubisz, Dennis Kostka)

DLESS: HMM-based detection of lineage-specific genomic elements
phyloP: Phylogenetic tests of lineage-specific selection with p-values
linAcc Code and Vignette: Model selection and testing for selection on multiple lineages

ProteinHistorian: Eukaryotic protein age estimation and enrichment analysis

Protein families

SFams updating software

MRC: Tools for building protein families and annotating metagenomes

Statistical Programming

R and Bioconductor Projects

multtest package (multiple hypothesis testing)
hopach package (clustering)

PAMSIL stand alone C program (clustering)


Niche modeling: Statistical prediction and mapping of geographic distributions

Spatial Autocorrelation: Testing for spatial structure in geographic distributions

Community Nestedness: Testing if communities have nested composition (versus differences due to turnover)

Genome Browsers

UCSC Genome Browser

UCSC Archaeal Genome Browser