:: DESCRIPTION
detectIR is a MATLAB-based tool for detecting perfect and imperfect inverted repeats in genomes.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
PLoS One. 2014 Nov 19;9(11):e113349. doi: 10.1371/journal.pone.0113349. eCollection 2014.
detectIR: a novel program for detecting perfect and imperfect inverted repeats using complex numbers and vector calculation.
Ye C, Ji G, Li L, Liang C
:: DESCRIPTION
PPH (Perfect Phylogeny Haplotyper based on graph realization ) is a program for inferring haplotypes from genotypes to determine if there are resulting haplotypes that fit a tree model (i.e. a perfect phylogeny, a coalescent). In more population genetic terms, PPH determines whether a set of SNP genotypes can be explained by haplotype pairs that could have evolved on a coalescent under the no-recombination, infinite sites model. Hence it determines for SNP genotype data what the three or four gametes test (depending on whether the tree is rooted or not) determines for haplotype data.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Ren Hua Chung and Dan Gusfield
Perfect Phylogeny Haplotyper: Haplotype Inferral Using a Tree Model
Bioinformatics (2003) 19 (6): 780-781.
:: DESCRIPTION
DPPH (Perfect Phylogeny Haplotyper: a direct method )is a program for inferring haplotypes from genotypes to determine if there are resulting haplotypes that fit a tree model (i.e. a perfect phylogeny, a coalescent). In more population genetic terms, DPPH determines whether a set of SNP genotypes can be explained by haplotype pairs that could have evolved on a coalescent under the no-recombination, infinite sites model. Hence it determines for SNP genotype data what the three or four gametes test (depending on whether the tree is rooted or not) determines for haplotype data.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bafna V, Gusfield D, Lancia G, Yooseph S.
Haplotyping as Perfect Phylogeny: A Direct Approach
J Comput Biol. 2003;10(3-4):323-40.
:: DESCRIPTION
LPPH (Linear-Time Algorithm for Perfect Phylogeny Haplotyping) is a linear-time program for inferring haplotypes from genotypes to determine if there are resulting haplotypes that fit a tree model.In more population genetic terms, LPPH determines whether a set of SNP genotypes can be explained by haplotype pairs that could have evolved on a coalescent under the no-recombination, infinite sites model. Hence it determines for SNP genotype data what the three or four gametes test (depending on whether the tree is rooted or not) determines for haplotype data.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
A linear-time algorithm to the Perfect Phylogeny Haplotyping (PPH) Problem.
Z. Ding, V. Filkov and D. Gusfield
J Comput Biol. 2006 Mar;13(2):522-53.
:: DESCRIPTION
BPPH (Perfect Phylogeny Haplotyper: The Berkeley method ) is a program for inferring haplotypes from genotypes to determine if there are resulting haplotypes that fit a tree model (i.e. a perfect phylogeny, a coalescent). In more population genetic terms, BPPH determines whether a set of SNP genotypes can be explained by haplotype pairs that could have evolved on a coalescent under the no-recombination, infinite sites model. Hence it determines for SNP genotype data what the three or four gametes test (depending on whether the tree is rooted or not) determines for haplotype data.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
“Haplotyping as Perfect Phylogeny: Conceptual Framework and Efficient Solutions”
D. Gusfield In Proceedings of RECOMB, Sixth Annual Conference on Research in Computational Molecular Biology, April 2002
