Software

• CT-CBN is a C program that implements algorithms for model selection and maximum likelihood parameter estimation of continuous time conjunctive Bayesian networks.

• deepSNV is an R package to test for low-frequency SNVs in deep sequencing experiments.

• Geno2pheno is a web server for the prediction of HIV phenotypic drug resistance and coreceptor usage from genotype.

• icbn is an R package for jointly estimating a conjunctive Bayesian network and an isotonic regression function on the induced genotype lattice from paired genotype-phenotype data.

• InDelFixer is a java program to remove frame shift causing insertions or deletions from next-generation sequencing data.

• MtreeHMM is a Perl program that implements an Expectation Maximization algorithm for estimating the parameters of the mutagenetic tree hidden Markov model from longitudinal clonal sequence data.

• Mtreemix is a software package for learning and using mutagenetic trees, a family of graphical models for the accumulation of mutations.

• ROCR is an R package for the visualization and ROC analysis of the performance of binary classifiers.

• QuasiRecomb is a java software to infer a viral quasispecies from Next Generation Sequencing (NGS) data.

• ShoRAH is a software package for inferring haplotypes and their frequencies from short sequence reads obtained from ultra-deep sequencing of a mixed sample.

• staRank is an R package for ranking variables according to their stability.