Please use this identifier to cite or link to this item:
http://hdl.handle.net/10261/1448
Share/Export:
![]() ![]() |
|
Visualizar otros formatos: MARC | Dublin Core | RDF | ORE | MODS | METS | DIDL | DATACITE | |
Title: | Topology testing of phylogenies using least squares methods |
Authors: | Czarna, Aleksandra; Sanjuán, Rafael CSIC ORCID; González-Candelas, Fernando; Wróbel, Borys | Issue Date: | 6-Dec-2006 | Publisher: | BioMed Central | Citation: | BMC Evolutionary Biology 2006, 6:105 | Abstract: | [Background] The least squares (LS) method for constructing confidence sets of trees is closely related to LS tree building methods, in which the goodness of fit of the distances measured on the tree (patristic distances) to the observed distances between taxa is the criterion used for selecting the best topology. The generalized LS (GLS) method for topology testing is often frustrated by the computational difficulties in calculating the covariance matrix and its inverse, which in practice requires approximations. The weighted LS (WLS) allows for a more efficient albeit approximate calculation of the test statistic by ignoring the covariances between the distances. [Results] The goal of this paper is to assess the applicability of the LS approach for constructing confidence sets of trees. We show that the approximations inherent to the WLS method did not affect negatively the accuracy and reliability of the test both in the analysis of biological sequences and DNA-DNA hybridization data (for which character-based testing methods cannot be used). On the other hand, we report several problems for the GLS method, at least for the available implementation. For many data sets of biological sequences, the GLS statistic could not be calculated. For some data sets for which it could, the GLS method included all the possible trees in the confidence set despite a strong phylogenetic signal in the data. Finally, contrary to WLS, for simulated sequences GLS showed undercoverage (frequent non-inclusion of the true tree in the confidence set). [Conclusion] The WLS method provides a computationally efficient approximation to the GLS useful especially in exploratory analyses of confidence sets of trees, when assessing the phylogenetic signal in the data, and when other methods are not available. |
URI: | http://hdl.handle.net/10261/1448 | DOI: | 10.1186/1471-2148-6-105 | ISSN: | 1471-2148 |
Appears in Collections: | (IBMCP) Artículos |
Files in This Item:
File | Description | Size | Format | |
---|---|---|---|---|
1471-2148-6-105.pdf | 404,81 kB | Adobe PDF | ![]() View/Open |
Review this work
SCOPUSTM
Citations
10
checked on May 10, 2022
WEB OF SCIENCETM
Citations
8
checked on May 12, 2022
Page view(s)
396
checked on May 15, 2022
Download(s)
115
checked on May 15, 2022
Google ScholarTM
Check
Altmetric
Dimensions
WARNING: Items in Digital.CSIC are protected by copyright, with all rights reserved, unless otherwise indicated.