Pollard Group -- Gladstone Institutes, UC San Francisco
 
 

Home

People

Research

Publications

Software

Positions

Contact



docpollard.com WWW
Software and Databases

Genome Browsers
UCSC Genome Browser

UCSC Archaeal Genome Browser

Pollard Lab Track Hubs
Hg19 Assembly
Hg18 Assembly
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

G-NEST: a gene neighborhood scoring tool to identify co-expressed, co-conserved genes
Examples
Galaxy instance: Click on "ucdavis" then "gnest" under "Tools".
Metagenomics
MetaPASSAGE: A Metagenomic Pipeline for Automated Simulations and Analysis of Gene Families

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

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

ShotMap: Tools for classifying shotgun metagenomic reads into protein families

Niche modeling: Statistical prediction of OTU distributions
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)
Github
Pollard Lab Github Repository