Software

One of the main activities of our group is to develop novel methods for analysing biological data, and to implement and test these methods. To ensure the maximum benefits of this effort to the field of bioinformatics, we strive to make the developed software readily available on very agreeable licensing terms. The implementation projects that have reached a level of maturity where we believe they will do less harm than good are listed below.

ParIS

This is a genome rearrangement server. It takes the gene orders and reading directions of two genomes and samples from the posterior probabilities of trajectories transforming the first genome into the second one using a Partial Importance Sampler technique, which is a version of the large class of Markov chain Monte Carlo methods.

Section 26

This is a software suite for parsimonious recombination analysis of single nucleotide polymorphism data under the infinite sites assumption. At the core is a branch & bound method for finding the exact minimum number of recombinations needed for a data set with an accompanying evolutionary history.

Pfold

This is an RNA fold server. It takes an alignment of RNA sequences as input and predicts a common structure for all sequences. The folding method uses a combination of rate matrices and a stochastic context free grammar.

IStVaN

Istvan is a collection of modules implementing various methods for inferring an invariant set, i.e. a set of genes with no or little difference in actual expression levels, from a set of pairs of microarray measured expression levels, and for inferring normalising functions based on a set of pairwise data, possibly an invariant set determined by one of the implemented methods.


CStoRM

This is a program for parsing a general hidden Markov model with a stochastic context free grammar. It is based on an extension of the CKY algorithm for parsing a sequence, and essentially finds the most probable combination of a path in the HMM and a parse tree in the SCFG under assumption of independence.

Rahnuma

Rahnuma is a tool for prediction and analysis of metabolic pathways and comparison of metabolic networks that represents metabolic networks as hypergraphs. Rahnuma computes all possible pathways between two or more metabolites by using constrained depth first traversal of a hypergraph. It also allows pathway based metabolic network comparisons at organism as well as phylogenetic level.

StatAlign

StatAlign is an extendable software package for Bayesian analysis of Protein, DNA and RNA sequences. Multiple alignments, phylogenetic trees and evolutionary parameters are co-estimated in a Markov Chain Monte Carlo framework, allowing for reliable measurement of the accuracy of the results. The models behind the analysis permit the comparison of evolutionarily distant sequences: the TKF92 insertion-deletion model can be coupled to an arbitrary substitution model.


Starfold

Starfold is a Java program for predicting RNA secondary structures including a class of pseudoknots. It requires a parameter file to be present. At the moment, running it directly from the JAR archive is only possible under 32-bit Windows.

Frnakenstein

Frnakenstein is a python program for solving the inverse RNA folding problem, i.e. given a target structure it attempts to design a sequence folding into this stucture.