Limits...
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.

Show MeSH
IDEA input GUI. IDEA's parameter input interface. Parameters for codeml or baseml are organized in three categories: data, model and other options. Mousing over the information icon next to a parameter brings up an explanation of that parameter (blue text box).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2655098&req=5

Figure 1: IDEA input GUI. IDEA's parameter input interface. Parameters for codeml or baseml are organized in three categories: data, model and other options. Mousing over the information icon next to a parameter brings up an explanation of that parameter (blue text box).

Mentions: An IDEA user first elects to run either codeml, which performs maximum likelihood analysis using codon substitution models, or baseml, which uses nucleotide substitution models. IDEA presents the parameters for the chosen PAML program grouped visually into three categories (data, model and other options) and allows the user to provide a value for each (Figure 1). Sensible default values are provided; the user may also load or save customized default values. A key to the interpretation of each parameter can be viewed by mousing over an icon next to that parameter's name (Figure 1). IDEA performs limited input validation to detect some common errors. A help menu connects the user to IDEA's online documentation.


IDEA: Interactive Display for Evolutionary Analyses.

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

IDEA input GUI. IDEA's parameter input interface. Parameters for codeml or baseml are organized in three categories: data, model and other options. Mousing over the information icon next to a parameter brings up an explanation of that parameter (blue text box).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 1: IDEA input GUI. IDEA's parameter input interface. Parameters for codeml or baseml are organized in three categories: data, model and other options. Mousing over the information icon next to a parameter brings up an explanation of that parameter (blue text box).
Mentions: An IDEA user first elects to run either codeml, which performs maximum likelihood analysis using codon substitution models, or baseml, which uses nucleotide substitution models. IDEA presents the parameters for the chosen PAML program grouped visually into three categories (data, model and other options) and allows the user to provide a value for each (Figure 1). Sensible default values are provided; the user may also load or save customized default values. A key to the interpretation of each parameter can be viewed by mousing over an icon next to that parameter's name (Figure 1). IDEA performs limited input validation to detect some common errors. A help menu connects the user to IDEA's online documentation.

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