Treemmer: a tool to reduce large phylogenetic datasets with minimal loss of diversity.
BMC Bioinformatics
; 19(1): 164, 2018 05 02.
Article
en En
| MEDLINE
| ID: mdl-29716518
ABSTRACT
BACKGROUND:
Large sequence datasets are difficult to visualize and handle. Additionally, they often do not represent a random subset of the natural diversity, but the result of uncoordinated and convenience sampling. Consequently, they can suffer from redundancy and sampling biases.RESULTS:
Here we present Treemmer, a simple tool to evaluate the redundancy of phylogenetic trees and reduce their complexity by eliminating leaves that contribute the least to the tree diversity.CONCLUSIONS:
Treemmer can reduce the size of datasets with different phylogenetic structures and levels of redundancy while maintaining a sub-sample that is representative of the original diversity. Additionally, it is possible to fine-tune the behavior of Treemmer including any kind of meta-information, making Treemmer particularly useful for empirical studies.Palabras clave
Texto completo:
1
Banco de datos:
MEDLINE
Asunto principal:
Virus de la Influenza A
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Filogenia
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Programas Informáticos
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Biología Computacional
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Mycobacterium tuberculosis
Límite:
Humans
Idioma:
En
Año:
2018
Tipo del documento:
Article