perfectphyloR: An R package for reconstructing perfect phylogenies.
BMC Bioinformatics
; 20(1): 729, 2019 Dec 23.
Article
em En
| MEDLINE
| ID: mdl-31870286
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 perfectphyloR 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 perfectphyloR 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.
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Base de dados:
MEDLINE
Assunto principal:
Filogenia
/
Evolução Molecular
Idioma:
En
Ano de publicação:
2019
Tipo de documento:
Article