Biological intuition in alignment-free methods: response to Posada

Ragan, Mark A. and Chan, Cheong Xin (2013) Biological intuition in alignment-free methods: response to Posada. Journal of Molecular Evolution, 77 1-2: 1-2. doi:10.1007/s00239-013-9573-0


Author Ragan, Mark A.
Chan, Cheong Xin
Title Biological intuition in alignment-free methods: response to Posada
Journal name Journal of Molecular Evolution   Check publisher's open access policy
ISSN 0022-2844
1432-1432
Publication date 2013-08-01
Year available 2013
Sub-type Letter to editor, brief commentary or brief communication
DOI 10.1007/s00239-013-9573-0
Volume 77
Issue 1-2
Start page 1
End page 2
Total pages 2
Place of publication New York, NY United States
Publisher Springer New York LLC
Language eng
Formatted abstract
A recent editorial in Journal of Molecular Evolution highlights opportunities and challenges facing molecular evolution in the era of next-generation sequencing. Abundant sequence data should allow more-complex models to be fit at higher confidence, making phylogenetic inference more reliable and improving our understanding of evolution at the molecular level. However, concern that approaches based on multiple sequence alignment may be computationally infeasible for large datasets is driving the development of so-called alignment-free methods for sequence comparison and phylogenetic inference. The recent editorial characterized these approaches as model-free, not based on the concept of homology, and lacking in biological intuition. We argue here that alignment-free methods have not abandoned models or homology, and can be biologically intuitive
Keyword Alignment free methods
Evolutionary models
Homology
Phylogenomics
Q-Index Code CX
Q-Index Status Provisional Code
Institutional Status UQ

Document type: Journal Article
Sub-type: Letter to editor, brief commentary or brief communication
Collection: Institute for Molecular Bioscience - Publications
 
Versions
Version Filter Type
Citation counts: TR Web of Science Citation Count  Cited 6 times in Thomson Reuters Web of Science Article | Citations
Scopus Citation Count Cited 5 times in Scopus Article | Citations
Google Scholar Search Google Scholar
Created: Thu, 01 Aug 2013, 20:43:39 EST by Susan Allen on behalf of Institute for Molecular Bioscience