:: DESCRIPTION
PTG is a heuristic algorithm that can find the minimum number of distinct haplotypes based on the criterion of keeping all genotypes resolved during tree-grow process.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Zhenping Li, Wenfeng Zhou, Xiangsun Zhang and Luonan Chen.
A parsimonious tree-grow method for haplotype inference.
Bioinformatics, Vol. 21, No. 17, pp. 3475-3481, 2005.
:: DESCRIPTION
HIT (Haplotype Inference Technique) solves so-called genotype phasing (or haplotype inference) problem. It estimates the haplotypes of a given set of genotypes consisting of SNPs (single nucleotide polymorhisms). It does this by learning a hidden Markov model for the haplotypes using an EM type algorithm.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Pasi Rastas, Mikko Koivisto, Heikki Mannila, and Esko Ukkonen:
Phasing genotypes using a hidden Markov model. In: I. Mandoiu and A. Zelikovsky (eds.),
Bioinformatics Algorithms: Techniques and Applications, pp. 373-391, Wiley 2008.
:: DESCRIPTION
HaploParser solves so-called genotype phasing (or haplotype inference) problem. The program (and its source) is mainly for educational and for research purposes.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Pasi Rastas, Esko Ukkonen
Haplotype Inference via Hierarchical Genotype Parsing
7th Workshop on Algorithms in Bioinformatics – WABI 2007
:: DESCRIPTION
BACH (BAyesian context-based Haplotype inference) solves so-called genotype phasing (or haplotype inference) problem. It is based on Bayesian approach to model haplotypes and genotypes with variable order Markov chains. It finds accurate haplotypes for given genotypes by Bayesian maximum a posterior criterion.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Pasi Rastas, Jussi Kollin, Mikko Koivisto
Fast Bayesian Haplotype Inference via Context Tree Weighting
K. Crandall, J. Lagergren (Eds.), Proc. 8th Workshop on Algorithms in Bioinformatics – WABI 2008, pp. 259-270.
