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Open Source Genomic Analysis for Phylogenetic Alignment and Search

This application allows users to perform genomic analysis through phylogenetic search and alignment operations. To utilize the software, you can either open a Nexus file from the file menu or access the command menu under the PSODA tab. Key references for PSODA and its incorporated software include foundational works in phylogenetic analysis and bioinformatics, ensuring a robust platform for researchers in the field. Enhance your genomic research with tools such as TreeSAAP and MRBAYES for efficient data handling and analysis.

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Open Source Genomic Analysis for Phylogenetic Alignment and Search

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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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