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Open Source Genomic Analysis

Open Source Genomic Analysis. To use this application, open a nexus file from file menu, or use the command menu under the PSODA tab to run alignment or phylogeny search. The following references can be used for PSODA and incorporated software.

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Open Source Genomic Analysis

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  1. Open Source Genomic Analysis To use this application, open a nexus file from file menu, or use the command menu under the PSODA tab to run alignment or phylogeny search. The following references can be used for PSODA and incorporated software. • Carroll, H., Teichert, A., Krein, J.,Sundberg, K.,Snell, Q.,Clement, M.,“An open source phylogenetic search and alignment package”, International Journal of Bioinformatics Research and Applications (IJBRA), Vol. 5, No. 3, 2009 • Woolley, S., Johnson, J., Smith, M., Crandall, K., McClellan, D. “TreeSAAP: Selection on Amino Acid Propertiesusing phylogenetic trees”, Bioinformatics, 19, 671-672 • Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), "The Jalview Java Alignment Editor", Bioinformatics, 20, 426-7. • Ronquist, F. and J. P. Huelsenbeck. 2003. MRBAYES 3: Bayesian phylogeneticinference under mixed models. Bioinformatics 19:1572-1574. • AlexandrosStamatakis, "RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models”, Bioinformatics 2006; doi: 10.1093/bioinformatics/btl446 • Zmasek, C. M. and Eddy, S. R. (2001). "ATV: display and manipulation of annotated phylogenetictrees" Bioinformatics, 17(4), 383-384.

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