Software

Metagenomics

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

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

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

Regulatory Genomics

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

TargetFinder: Enhancer-promoter 3D interaction models

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

Examples
Galaxy instance: Click on “ucdavis” then “gnest” under “Tools”.

Comparative & Population Genomics

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: 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)
rphast package (phylogenetic analysis with space/time models) (also on CRAN)

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 Genome Browser

UCSC Archaeal Genome Browser