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. 2010 May 27;11:284. doi: 10.1186/1471-2105-11-284

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Copyright ©2010 Steinway et al; licensee BioMed Central Ltd.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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JCoDA interface. A) The JCoDA interface accepts cDNA in FASTA format and JCoDA manages the generation of codon delimited alignments, pairwise or site-based dN/dS calculation through PAML, and graphing of either output (top). The codon delimited alignment tab is shown. Common options are displayed on the main interface and the file menu contains export options. Outputs, such as raw data, alignments, and graphs are displayed in tabbed panes for easy navigation. Graphs for multiple models are retained in the tabbed interface for comparison. For pairwise dN/dS the user the selects sequences from a list using add/remove buttons. The advanced options check box provides direct access to the codeml control file as a tabbed pane. For site-based analysis JCoDA defaults to implement models M7 (null, neutral) -vs- M8 (alternate, selection) in codeml. The user can set the path for their own tree file or use the PHYLIP graphical interface (PGI) to generate phylogenetic a tree (bottom).