HaploPool specifications

Information


Unique identifier OMICS_31605
Name HaploPool
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages MATLAB, Perl
Computer skills Advanced
Stability Stable
Requirements
GCC/G++
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Bonnie Kirkpatrick

Publication for HaploPool

HaploPool citations

 (2)
library_books

Maximum parsimony haplotype frequencies inference based on a joint constrained sparse representation of pooled DNA

2013
BMC Bioinformatics
PMCID: 3847492
PMID: 24010487
DOI: 10.1186/1471-2105-14-270

[…] mall pool sizes mainly contains methods that use the expectation-maximization (EM) algorithm for maximizing the multinomial likelihood [-]. Kirkpatrick et al. [] suggested a perfect phylogeny method, HAPLOPOOL, that was supplemented with the EM algorithm and linear regression in order to combine haplotype segments and was shown to outperform competing EM algorithms.Haplotype frequency estimation f […]

library_books

Fast and accurate haplotype frequency estimation for large haplotype vectors from pooled DNA data

2012
BMC Genet
PMCID: 3560217
PMID: 23110720
DOI: 10.1186/1471-2156-13-94

[…] o estimate the haplotypes. A method based on perfect phylogeny, HAPLOPOOL, was suggested in [] and was supplemented with the EM algorithm and linear regression in order to combine haplotype segments. HAPLOPOOL has demonstrated superior performance in terms of accuracy and computational time with respect to the competing EM algorithms. The second category consists of methods that focus on large poo […]

HaploPool institution(s)
Department of Electrical Engineering and Computer Sciences, UC Berkeley, Berkeley, CA, USA; Computer Science Department, Universidad Rey Juan Carlos, Madrid, Spain; International Computer Science Institute, Berkeley, Berkeley, CA, USA
HaploPool funding source(s)
Supported by a DOE Computational Science Graduate Fellowship under grant number DE-FG02-97ER25308 and by NSF grant IIS0513599.

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