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BMC Bioinformatics. 2014 Nov 8;15:354. doi: 10.1186/s12859-014-0354-6.

MLGO: phylogeny reconstruction and ancestral inference from gene-order data.

Hu F1,2, Lin Y3, Tang J4,5.

Author information

1
Tianjin Key Laboratory of Cognitive Computing and Application, Tianjin University, Tianjin, 300072, China. hufeiyc@gmail.com.
2
Department of Computer Science and Engineering, University of South Carolina, Columbia, 29208, SC, USA. hufeiyc@gmail.com.
3
Department of Computer Science and Engineering, University of California, San Diego, 92093 La Jolla, CA, USA. yul280@ucsd.edu.
4
Tianjin Key Laboratory of Cognitive Computing and Application, Tianjin University, Tianjin, 300072, China. jtang@ces.sc.edu.
5
Department of Computer Science and Engineering, University of South Carolina, Columbia, 29208, SC, USA. jtang@ces.sc.edu.

Abstract

BACKGROUND:

The rapid accumulation of whole-genome data has renewed interest in the study of using gene-order data for phylogenetic analyses and ancestral reconstruction. Current software and web servers typically do not support duplication and loss events along with rearrangements.

RESULTS:

MLGO (Maximum Likelihood for Gene-Order Analysis) is a web tool for the reconstruction of phylogeny and/or ancestral genomes from gene-order data. MLGO is based on likelihood computation and shows advantages over existing methods in terms of accuracy, scalability and flexibility.

CONCLUSIONS:

To the best of our knowledge, it is the first web tool for analysis of large-scale genomic changes including not only rearrangements but also gene insertions, deletions and duplications. The web tool is available from http://www.geneorder.org/server.php .

PMID:
25376663
PMCID:
PMC4236499
DOI:
10.1186/s12859-014-0354-6
[Indexed for MEDLINE]
Free PMC Article

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