ProtTest 3: fast selection of best-fit models of protein evolution

Bioinformatics - Tập 27 Số 8 - Trang 1164-1165 - 2011
Diego Darriba1, Guillermo L. Taboada1, Ramón Doallo1, David Posada1
11 Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310 Vigo and 2Department of Electronics and Systems, Computer Architecture Group, University of A Coruña, 15071 A Coruña, Spain

Tóm tắt

Abstract Summary: We have implemented a high-performance computing (HPC) version of ProtTest that can be executed in parallel in multicore desktops and clusters. This version, called ProtTest 3, includes new features and extended capabilities. Availability: ProtTest 3 source code and binaries are freely available under GNU license for download from http://darwin.uvigo.es/software/prottest3, linked to a Mercurial repository at Bitbucket (https://bitbucket.org/). Contact:  [email protected] Supplementary information:  Supplementary data are available at Bioinformatics online.

Từ khóa


Tài liệu tham khảo

Abascal, 2007, ProtTest: selection of best-fit models of protein evolution, Bioinformatics, 24, 1104

Dagum, 1998, OpenMP: an industry-standard API for shared-memory programming, IEEE Comput. Sci. Eng., 5, 46, 10.1109/99.660313

Drummond, 2001, Pal: an object-oriented programming library for molecular evolution and phylogenetics, Bioinformatics, 17, 662, 10.1093/bioinformatics/17.7.662

Glez-Peña, 2010, ALTER: program-oriented conversion of DNA and protein alignments, Nucleic Acids Res., 38, W14, 10.1093/nar/gkq321

Guindon, 2003, A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood, Syst. Biol., 52, 696, 10.1080/10635150390235520

Posada, 2004, Model selection and model averaging in phylogenetics: advantages of akaike information criterion and bayesian approaches over likelihood ratio tests, Syst. Biol., 53, 793, 10.1080/10635150490522304

Shafi, 2009, Nested parallelism for multi-core HPC systems using Java, J. Parallel Distr. Com., 69, 532, 10.1016/j.jpdc.2009.02.006

Sullivan, 2005, Model selection in phylogenetics, Annu. Rev. Ecol. Evol. S, 36, 445, 10.1146/annurev.ecolsys.36.102003.152633

Thông tin
Thông tin xuất bản

Bioinformatics

Tập 27 Số 8

1164-1165

Thông tin tác giả