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Software and Databases
Genome Browsers
UCSC Genome Browser
UCSC Archaeal Genome Browser
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
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)
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