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Open Access Highly Accessed Methodology article

PICS-Ord: unlimited coding of ambiguous regions by pairwise identity and cost scores ordination

Robert Lücking1*, Brendan P Hodkinson2, Alexandros Stamatakis3 and Reed A Cartwright4

Author affiliations

1 Department of Botany, The Field Museum, 1400 South Lake Shore Drive, Chicago, IL 60605-2496, USA

2 Department of Biology, Box 90338, Duke University, Durham, NC 27708-0338, USA

3 The Exelixis Lab, Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, D-69118, Heidelberg, Germany

4 Department of Biology and Biochemistry, University of Houston, 369 Science & Research Bldg 2, Houston, TX 77204-5001, USA

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Citation and License

BMC Bioinformatics 2011, 12:10  doi:10.1186/1471-2105-12-10

Published: 7 January 2011

Abstract

Background

We present a novel method to encode ambiguously aligned regions in fixed multiple sequence alignments by 'Pairwise Identity and Cost Scores Ordination' (PICS-Ord). The method works via ordination of sequence identity or cost scores matrices by means of Principal Coordinates Analysis (PCoA). After identification of ambiguous regions, the method computes pairwise distances as sequence identities or cost scores, ordinates the resulting distance matrix by means of PCoA, and encodes the principal coordinates as ordered integers. Three biological and 100 simulated datasets were used to assess the performance of the new method.

Results

Including ambiguous regions coded by means of PICS-Ord increased topological accuracy, resolution, and bootstrap support in real biological and simulated datasets compared to the alternative of excluding such regions from the analysis a priori. In terms of accuracy, PICS-Ord performs equal to or better than previously available methods of ambiguous region coding (e.g., INAASE), with the advantage of a practically unlimited alignment size and increased analytical speed and the possibility of PICS-Ord scores to be analyzed together with DNA data in a partitioned maximum likelihood model.

Conclusions

Advantages of PICS-Ord over step matrix-based ambiguous region coding with INAASE include a practically unlimited number of OTUs and seamless integration of PICS-Ord codes into phylogenetic datasets, as well as the increased speed of phylogenetic analysis. Contrary to word- and frequency-based methods, PICS-Ord maintains the advantage of pairwise sequence alignment to derive distances, and the method is flexible with respect to the calculation of distance scores. In addition to distance and maximum parsimony, PICS-Ord codes can be analyzed in a Bayesian or maximum likelihood framework. RAxML (version 7.2.6 or higher that was developed for this study) allows up to 32-state ordered or unordered characters. A GTR, MK, or ORDERED model can be applied to analyse the PICS-Ord codes partition, with GTR performing slightly better than MK and ORDERED.

Availability

An implementation of the PICS-Ord algorithm is available from http://scit.us/projects/ngila/wiki/PICS-Ord webcite. It requires both the statistical software, R http://www.r-project.org webcite and the alignment software Ngila http://scit.us/projects/ngila webcite.