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IDEA: Interactive Display for Evolutionary Analyses.

Egan A, Mahurkar A, Crabtree J, Badger JH, Carlton JM, Silva JC - BMC Bioinformatics (2008)

Bottom Line: A significant drawback of these programs is their lack of a graphical user interface, which can limit their user base and considerably reduce their efficiency.Novel options streamline the analysis process, and post-analysis visualization of phylogenies, evolutionary rates and selective constraint along protein sequences simplifies the interpretation of results.The integration of these functions into a single tool eliminates the need for lengthy data handling and parsing, significantly expediting access to global patterns in the data.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA. aegan@som.umaryland.edu

ABSTRACT

Background: The availability of complete genomic sequences for hundreds of organisms promises to make obtaining genome-wide estimates of substitution rates, selective constraints and other molecular evolution variables of interest an increasingly important approach to addressing broad evolutionary questions. Two of the programs most widely used for this purpose are codeml and baseml, parts of the PAML (Phylogenetic Analysis by Maximum Likelihood) suite. A significant drawback of these programs is their lack of a graphical user interface, which can limit their user base and considerably reduce their efficiency.

Results: We have developed IDEA (Interactive Display for Evolutionary Analyses), an intuitive graphical input and output interface which interacts with PHYLIP for phylogeny reconstruction and with codeml and baseml for molecular evolution analyses. IDEA's graphical input and visualization interfaces eliminate the need to edit and parse text input and output files, reducing the likelihood of errors and improving processing time. Further, its interactive output display gives the user immediate access to results. Finally, IDEA can process data in parallel on a local machine or computing grid, allowing genome-wide analyses to be completed quickly.

Conclusion: IDEA provides a graphical user interface that allows the user to follow a codeml or baseml analysis from parameter input through to the exploration of results. Novel options streamline the analysis process, and post-analysis visualization of phylogenies, evolutionary rates and selective constraint along protein sequences simplifies the interpretation of results. The integration of these functions into a single tool eliminates the need for lengthy data handling and parsing, significantly expediting access to global patterns in the data.

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Process monitor. The Workflow Monitor allows the user to see which processes are running and peruse command output as it is generated. A hierarchy of jobs to be executed is displayed on the left. Clicking on a node on the left produces a detailed report on the execution status of that job or subset of jobs on the right. Information available includes start time, end time, execution host, percentage of jobs completed, execution time and command-line output.
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Figure 3: Process monitor. The Workflow Monitor allows the user to see which processes are running and peruse command output as it is generated. A hierarchy of jobs to be executed is displayed on the left. Clicking on a node on the left produces a detailed report on the execution status of that job or subset of jobs on the right. Information available includes start time, end time, execution host, percentage of jobs completed, execution time and command-line output.

Mentions: Once the computational utility and parameters are specified, the IDEA pipeline processes each dataset (typically a set of orthologs) in four steps (Figure 2). The user may monitor the progress of an analysis by summoning the graphical monitor, a part of the Workflow process-management suite (Figure 3). Icons indicate which steps of the process are running, completed or waiting to start. The View Outand View Err buttons allow the user to see the complete command-line output of each process.


IDEA: Interactive Display for Evolutionary Analyses.

Egan A, Mahurkar A, Crabtree J, Badger JH, Carlton JM, Silva JC - BMC Bioinformatics (2008)

Process monitor. The Workflow Monitor allows the user to see which processes are running and peruse command output as it is generated. A hierarchy of jobs to be executed is displayed on the left. Clicking on a node on the left produces a detailed report on the execution status of that job or subset of jobs on the right. Information available includes start time, end time, execution host, percentage of jobs completed, execution time and command-line output.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2655098&req=5

Figure 3: Process monitor. The Workflow Monitor allows the user to see which processes are running and peruse command output as it is generated. A hierarchy of jobs to be executed is displayed on the left. Clicking on a node on the left produces a detailed report on the execution status of that job or subset of jobs on the right. Information available includes start time, end time, execution host, percentage of jobs completed, execution time and command-line output.
Mentions: Once the computational utility and parameters are specified, the IDEA pipeline processes each dataset (typically a set of orthologs) in four steps (Figure 2). The user may monitor the progress of an analysis by summoning the graphical monitor, a part of the Workflow process-management suite (Figure 3). Icons indicate which steps of the process are running, completed or waiting to start. The View Outand View Err buttons allow the user to see the complete command-line output of each process.

Bottom Line: A significant drawback of these programs is their lack of a graphical user interface, which can limit their user base and considerably reduce their efficiency.Novel options streamline the analysis process, and post-analysis visualization of phylogenies, evolutionary rates and selective constraint along protein sequences simplifies the interpretation of results.The integration of these functions into a single tool eliminates the need for lengthy data handling and parsing, significantly expediting access to global patterns in the data.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA. aegan@som.umaryland.edu

ABSTRACT

Background: The availability of complete genomic sequences for hundreds of organisms promises to make obtaining genome-wide estimates of substitution rates, selective constraints and other molecular evolution variables of interest an increasingly important approach to addressing broad evolutionary questions. Two of the programs most widely used for this purpose are codeml and baseml, parts of the PAML (Phylogenetic Analysis by Maximum Likelihood) suite. A significant drawback of these programs is their lack of a graphical user interface, which can limit their user base and considerably reduce their efficiency.

Results: We have developed IDEA (Interactive Display for Evolutionary Analyses), an intuitive graphical input and output interface which interacts with PHYLIP for phylogeny reconstruction and with codeml and baseml for molecular evolution analyses. IDEA's graphical input and visualization interfaces eliminate the need to edit and parse text input and output files, reducing the likelihood of errors and improving processing time. Further, its interactive output display gives the user immediate access to results. Finally, IDEA can process data in parallel on a local machine or computing grid, allowing genome-wide analyses to be completed quickly.

Conclusion: IDEA provides a graphical user interface that allows the user to follow a codeml or baseml analysis from parameter input through to the exploration of results. Novel options streamline the analysis process, and post-analysis visualization of phylogenies, evolutionary rates and selective constraint along protein sequences simplifies the interpretation of results. The integration of these functions into a single tool eliminates the need for lengthy data handling and parsing, significantly expediting access to global patterns in the data.

Show MeSH