The PISAtoolbox is a set of executables which provide the user a rich set of methods for the analysis of biological sequence data. The basic workflow of a typical analysis is to first build a probabilistic model from a set of sequences and then use other programs to simulate sequences or predict new sequences.The PISA sofware toolbox is devoted to large-scale sequence analysis using a special class of probabilistic models, so-called Variable Order Markov Chains (VOMCs). It is based on efficient algorithms which use state-of-the-art sequence indices, like suffix trees and suffix arrays, to achieve high runtime performance for arbitrary parameter settings and sequence lengths.
- Linux / Windows
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Marcel H. Schulz, David Weese, Tobias Rausch, Andreas Döring, Knut Reinert and Martin Vingron.
Fast and Adaptive Variable Order Markov Chain Construction.
Proceedings of the 8th International Workshop in Algorithms in Bioinformatics (WABI’08) , page 306-317.