Software


TaxADivA
TaxADivA TAXonomy Assignment and DIVersity Assessment




stringMLST
stringMLST An fast k-mer based MLST tool
Bioinformatics doi: 10.1093/bioinformatics/btw586 (In press)



BroadPeak
BroadPeak broad peak calling algorithm for diffuse ChIP-seq datasets.




ChAT - unsupervised algorithm to search combinatorial chromatin signatures.



chipseq mapper

ChIP-seq ambiguous tag mapper - a Gibbs sampling algorithm for the mapping of ambiguous ChIP-seq sequence tags. A collaboration with the Lunyak laboratory at the Buck Institute for Age Research.
Bioinformatics 26: 2501-2508 [PubMed] [PDF] [Google Scholar]



MGIP

MGIP - a suite of computational tools for the analysis of multi-locus sequence typing (MLST) data. A collaboration with the Meningitis Laboratory at the Centers for Disease Control and Prevention.
Nucleic Acids Res 37: W606-W611 [PubMed] [PDF] [Google Scholar]



MGIP

Computational Genomics Pipeline - an analytical pipeline for the analysis of prokaryotic genome sequences. Includes genome assembly, gene prediction and fucntional annotation. A collaboration with the Meningitis Laboratory at the Centers for Disease Control and Prevention.
Bioinformatics 26: 1819-1826 [PubMed] [PDF] [Google Scholar]


nbase

Neisseria Base - An online comparative genomics browser for Neisseria spp. A collaboration with the Meningitis Laboratory at the Centers for Disease Control and Prevention.
Database 2011: bar 035 [PubMed] [PDF] [Goolge Scholar]


haemobase

HaemoBase a Haemophilus haemolyticus genome database. HeaemoBase includes genome and clinical data on five Haemophilus haemolyticus (Hhae) strains and one non-typeable influenzae (NTHi) strain.