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Barking Up The Wrong Treelength: The Impact of Gap Penalty on Alignment and Tree Accuracy
January-March 2009 (vol. 6 no. 1)
pp. 7-21
ASCII Text
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Kevin Liu, Serita Nelesen, Sindhu Raghavan, C. Randal Linder, Tandy Warnow, "Barking Up The Wrong Treelength: The Impact of Gap Penalty on Alignment and Tree Accuracy," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 6, no. 1, pp. 7-21, January-March, 2009.
 
 
BibTex
x
 
@article{ 10.1109/TCBB.2008.63,
author = {Kevin Liu and Serita Nelesen and Sindhu Raghavan and C. Randal Linder and Tandy Warnow},
title = {Barking Up The Wrong Treelength: The Impact of Gap Penalty on Alignment and Tree Accuracy},
journal ={IEEE/ACM Transactions on Computational Biology and Bioinformatics},
volume = {6},
number = {1},
issn = {1545-5963},
year = {2009},
pages = {7-21},
doi = {http://doi.ieeecomputersociety.org/10.1109/TCBB.2008.63},
publisher = {IEEE Computer Society},
address = {Los Alamitos, CA, USA},
}
 
 
RefWorks Procite/RefMan/Endnote
x 
 
TY - JOUR
JO - IEEE/ACM Transactions on Computational Biology and Bioinformatics
TI - Barking Up The Wrong Treelength: The Impact of Gap Penalty on Alignment and Tree Accuracy
IS - 1
SN - 1545-5963
SP7
EP21
EPD - 7-21
A1 - Kevin Liu,
A1 - Serita Nelesen,
A1 - Sindhu Raghavan,
A1 - C. Randal Linder,
A1 - Tandy Warnow,
PY - 2009
KW - Markov processes
KW - Biology and genetics
VL - 6
JA - IEEE/ACM Transactions on Computational Biology and Bioinformatics
ER -
 
Kevin Liu, The University of Texas at Austin, Austin
Serita Nelesen, The University of Texas at Austin, Austin
Sindhu Raghavan, The University of Texas at Austin, Austin
C. Randal Linder, The University of Texas at Austin, Austin
Tandy Warnow, The University of Texas at Austin, Austin
Several methods have been developed for simultaneous estimation of alignment and tree, of which POY is the most popular. In a 2007 paper published in Systematic Biology, Ogden and Rosenberg reported on a simulation study in which they compared POY to estimating the alignment using ClustalW and then analyzing the resultant alignment using maximum parsimony. They found that ClustalW+MP outperformed POY with respect to alignment and phylogenetic tree accuracy, and they concluded that simultaneous estimation techniques are not competitive with two-phase techniques. Our paper presents a simulation study in which we focus on the NP-hard optimization problem that POY addresses: minimizing treelength. Our study considers the impact of the gap penalty and suggests that the poor performance observed for POY by Ogden and Rosenberg is due to the simple gap penalties they used to score alignment/tree pairs. Our study suggests that optimizing under an affine gap penalty might produce alignments that are better than ClustalW alignments, and competitive with those produced by the best current alignment methods. We also show that optimizing under this affine gap penalty produces trees whose topological accuracy is better than ClustalW+MP, and competitive with the current best two-phase methods.

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Index Terms:
Markov processes, Biology and genetics
Citation:
Kevin Liu, Serita Nelesen, Sindhu Raghavan, C. Randal Linder, Tandy Warnow, "Barking Up The Wrong Treelength: The Impact of Gap Penalty on Alignment and Tree Accuracy," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 6, no. 1, pp. 7-21, Jan.-March 2009, doi:10.1109/TCBB.2008.63
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