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Software and Databases

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

SFam: A large, phylogenetically diverse protein-family resouce
Database
Updating software
VFam: A phylogenetically diverse viral protein-family resouce

MRC: Tools for building protein families and annotating metagenomes

Niche modeling: Statistical prediction and mapping of geographic distributions

Spatial Autocorrelation: Testing for spatial structure in geographic distributions

Regulatory Genomics
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 Genomics
PHAST package (with Adam Siepel)
DLESS: HMM-based detection of lineage-specific genomic elements
phyloP: Phylogenetic tests of lineage-specific selection with p-values
ProteinHistorian: Eukaryotic protein age estimation and enrichment analysis

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)
Genome Browsers
UCSC Genome Browser

UCSC Archaeal Genome Browser

Pollard Lab Track Hubs
Hg19 Assembly
Hg18 Assembly