Software
Metagenomics
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
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)
Ecology
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 Archaeal Genome Browser