2009 · Bioinformatics
Peter Cock, Tiago Antão, Jeffrey T. Chang, Brad Chapman, Cymon J. Cox, Andrew Dalke, Iddo Friedberg, Thomas Hamelryck, Frank…
Abstract Summary: The Biopython project is a mature open source international collaboration of volunteer developers, providing Python libraries for a wide range of bioinformatics problems. Biopython includes modules for reading and writing different sequence file formats and multiple sequence alignments, dealing with 3D macro molecular structures, interacting with common tools such as BLAST, ClustalW and EMBOSS, accessing key online databases, as well as providing numerical methods for statistical learning. Availability: Biopython is freely available, with documentation and source code at www.biopython.org under the Biopython license. Contact: All queries should be directed to the Biopython mailing lists, see www.biopython.org/wiki/_Mailing_listspeter.cock@scri.ac.uk.
6,696 citations2 viewsFull text
DOI: 10.1093/bioinformatics/btp1632003 · Bioinformatics
Fredrik Ronquist, John P. Huelsenbeck
Abstract Summary: MrBayes 3 performs Bayesian phylogenetic analysis combining information from different data partitions or subsets evolving under different stochastic evolutionary models. This allows the user to analyze heterogeneous data sets consisting of different data types—e.g. morphological, nucleotide, and protein—and to explore a wide variety of structured models mixing partition-unique and shared parameters. The program employs MPI to parallelize Metropolis coupling on Macintosh or UNIX clusters. Availability: http://morphbank.ebc.uu.se/mrbayes Contact: fredrik.ronquist@ebc.uu.se * To whom correspondence should be addressed.
29,493 citations2 viewsFull text
DOI: 10.1093/bioinformatics/btg1802003 · Bioinformatics
Michael Hucka, Andrew Finney, Herbert M. Sauro, Hamid Bolouri, John C. Doyle, Hiroaki Kitano, Adam P. Arkin, B. Bornstein, D…
MOTIVATION: Molecular biotechnology now makes it possible to build elaborate systems models, but the systems biology community needs information standards if models are to be shared, evaluated and developed cooperatively. RESULTS: We summarize the Systems Biology Markup Language (SBML) Level 1, a free, open, XML-based format for representing biochemical reaction networks. SBML is a software-independent language for describing models common to research in many areas of computational biology, including cell signaling pathways, metabolic pathways, gene regulation, and others. AVAILABILITY: The specification of SBML Level 1 is freely available from http://www.sbml.org/
3,170 citations2 viewsFull text
DOI: 10.1093/bioinformatics/btg0151998 · Bioinformatics
Sean R. Eddy
The recent literature on profile hidden Markov model (profile HMM) methods and software is reviewed. Profile HMMs turn a multiple sequence alignment into a position-specific scoring system suitable for searching databases for remotely homologous sequences. Profile HMM analyses complement standard pairwise comparison methods for large-scale sequence analysis. Several software implementations and two large libraries of profile HMMs of common protein domains are available. HMM methods performed comparably to threading methods in the CASP2 structure prediction exercise.
5,837 citations1 viewsFull text
DOI: 10.1093/bioinformatics/14.9.7551998 · Bioinformatics
David Posada, Keith A. Crandall
SUMMARY: The program MODELTEST uses log likelihood scores to establish the model of DNA evolution that best fits the data. AVAILABILITY: The MODELTEST package, including the source code and some documentation is available at http://bioag.byu. edu/zoology/crandall_lab/modeltest.html.
20,127 citations2 views
DOI: 10.1093/bioinformatics/14.9.817