Fast Perfect Phylogeny Haplotype Inference

2003 ◽  
pp. 183-194 ◽  
Author(s):  
Peter Damaschke
Keyword(s):  
Haplotype Inference ◽  
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.

scholarly journals A New Method for Haplotype Inference Including Full-Sib Information

Genetics ◽  
2007 ◽  
Vol 177 (3) ◽  
pp. 1929-1940 ◽  
Author(s):  
Xiang Dong Ding ◽  
Henner Simianer ◽  
Qin Zhang
Keyword(s):  
Haplotype Inference ◽  
New Method

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 A haplotype inference algorithm for trios based on deterministic sampling

BMC Genetics ◽  
2010 ◽  
Vol 11 (1) ◽  
pp. 78 ◽  
Author(s):  
Alexandros Iliadis ◽  
John Watkinson ◽  
Dimitris Anastassiou ◽  
Xiaodong Wang
Keyword(s):  
Haplotype Inference ◽  
Inference Algorithm ◽  
Deterministic Sampling
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