scholarly journals The Three-state Perfect Phylogeny Problem Reduces to 2-SAT

2009 ◽  
Vol 9 (4) ◽  
pp. 295-302
Author(s):  
Dan Gusfield ◽  
Yufeng Wu
Keyword(s):  
Perfect Phylogeny

scholarly journals perfectphyloR: An R package for reconstructing perfect phylogenies

2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Charith B. Karunarathna ◽  
Jinko Graham
Keyword(s):  
Binary Tree ◽  
Sequence Data ◽  
R Package ◽  
Binary Sequences ◽  
Ancestral Haplotype ◽  
Perfect Phylogeny ◽  
Nested Partitions ◽  
Genetic Sequence ◽  
Insight Into ◽  
Rooted Binary Tree

Abstract Background A perfect phylogeny is a rooted binary tree that recursively partitions sequences. The nested partitions of a perfect phylogeny provide insight into the pattern of ancestry of genetic sequence data. For example, sequences may cluster together in a partition indicating that they arise from a common ancestral haplotype. Results We present an R package to reconstruct the local perfect phylogenies underlying a sample of binary sequences. The package enables users to associate the reconstructed partitions with a user-defined partition. We describe and demonstrate the major functionality of the package. Conclusion The package should be of use to researchers seeking insight into the ancestral structure of their sequence data. The reconstructed partitions have many applications, including the mapping of trait-influencing variants.

Computational Problems in Perfect Phylogeny Haplotyping: Xor-Genotypes and Tag SNPs

2004 ◽  
pp. 14-31 ◽  
Author(s):  
Tamar Barzuza ◽  
Jacques S. Beckmann ◽  
Ron Shamir ◽  
Itsik Pe’er
Keyword(s):  
Perfect Phylogeny ◽  
Tag Snps

A Novel Insight into the Perfect Phylogeny Problem

2006 ◽  
Vol 10 (1) ◽  
pp. 97-109 ◽  
Author(s):  
S. Grünewald ◽  
K. T. Huber
Keyword(s):  
Perfect Phylogeny ◽  
Insight Into

scholarly journals Bayesian logistic regression using a perfect phylogeny

Biostatistics ◽  
2006 ◽  
Vol 8 (1) ◽  
pp. 32-52 ◽  
Author(s):  
T. G. Clark ◽  
M. De Iorio ◽  
R. C. Griffiths
Keyword(s):  
Logistic Regression ◽  
Perfect Phylogeny ◽  
Bayesian Logistic Regression
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