Software

BAPS: software for Bayesian Analysis of genetic Population Structure BIB: Bayesian Identification of Bacterial strains from sequencing data biMM: Efficient estimation of genetic variances and covariances for cohorts with high-dimensional phenotype measurements. BitSeq: Transcript isoform level expression and differential expression estimation for RNA-seq BRATNextGen: software for Bayesian modeling of recombination events based on whole-genome data FINEMAP: Efficient variable selection using summary data from genome-wide association studies. genomeDCA: software for inferring epistatic interactions from bacterial population genomic data. GPstuff: Gaussian process models for Bayesian analysis SEER: software for bacterial pangenomic GWAS.

BANANAS: software for inferring population trees based on molecular marker data. BASTA: software for Bayesian modeling of DNA copy number amplification data BEBaC: software for estimating bacterial community composition from 454 sequencing data biMM: Efficient estimation of genetic variances and covariances for cohorts with high-dimensional phenotype measurements. Biolog Decomposition: R package for decomposing Biolog PM data. BRAT: software for Bayesian modeling of recombination events GPrank: Gaussian Process Ranking of Multiple Time Series K-PAX software for Bayesian unsupervised classification of protein sequences metaCCA: Multivariate meta-analysis of genome-wide association studies using canonical correlation analysis MMM: Linear mixed model software R-Biolog: R package for analysing Biolog PM data T-BAPS: software for Bayesian Analysis of genetic Population Structure using T-RFLP markers tigre: Transcription factor Inference through Gaussian process Reconstruction of Expression tigreBrowser: web-based browser for genomic time course modelling results