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IDEA: Interactive Display for Evolutionary Analyses
- Source :
- BMC Bioinformatics, Vol 9, Iss 1, p 524 (2008), BMC Bioinformatics
- Publication Year :
- 2008
- Publisher :
- BMC, 2008.
-
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.
- Subjects :
- 0106 biological sciences
Plasmodium
Theoretical computer science
Biology
Machine learning
computer.software_genre
lcsh:Computer applications to medicine. Medical informatics
010603 evolutionary biology
01 natural sciences
Biochemistry
Evolution, Molecular
03 medical and health sciences
User-Computer Interface
Structural Biology
Phylogenetics
Molecular evolution
Databases, Genetic
Animals
Limit (mathematics)
Molecular Biology
lcsh:QH301-705.5
Phylogeny
030304 developmental biology
Graphical user interface
0303 health sciences
Internet
Phylogenetic tree
Models, Genetic
business.industry
Applied Mathematics
Suite
Substitution (logic)
Genomics
Sequence Analysis, DNA
Computer Science Applications
lcsh:Biology (General)
Data Interpretation, Statistical
lcsh:R858-859.7
Artificial intelligence
business
computer
Software
Drawback
Subjects
Details
- Language :
- English
- ISSN :
- 14712105
- Volume :
- 9
- Issue :
- 1
- Database :
- OpenAIRE
- Journal :
- BMC Bioinformatics
- Accession number :
- edsair.doi.dedup.....1628a896101e3d17f22e0139b34d7732