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A Practical Guide to Phylogenetics for Nonexperts
Published on: February 5, 2014
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Integrated Automatic Workflow for Phylogenetic Tree Analysis Using Public Access and Local Web Services.
Journal of Integrative Bioinformatics
|February 11, 2017
Summary
This study introduces an automated Taverna workflow for phylogenetic tree inference using coding sequences (CDS). The workflow efficiently analyzes large datasets, providing rapid and reliable phylogenetic analysis for bioinformaticians.
Area of Science:
- Bioinformatics
- Computational Biology
- Genomics
Background:
- Coding sequences (CDS) are increasingly discovered, necessitating advanced phylogenetic tree analysis tools.
- Existing tools require frequent upgrades, driving the need for integrated and automated solutions.
Purpose of the Study:
- To develop an integrated, automatic Taverna workflow for phylogenetic tree inference.
- To leverage public and local web services for enhanced CDS analysis.
Main Methods:
- Developed an automated Taverna workflow accepting CDS in Fasta format.
- Integrated public web services (EMBL-EBI, SIB) and local web services (Soaplab2, Apache Axis2).
- Implemented Parsimony, Distance Matrix-Neighbor Joining, and Maximum Likelihood algorithms with a novel MSA similarity score.
Main Results:
- The workflow supports 1,000 to 20,000 bootstrapping replicates.
- Achieved execution times under ten minutes for 10,000 bootstrap replicates.
- Validated workflow performance and verified results.
Conclusions:
- The proposed integrated workflow offers efficient and automated phylogenetic tree inferring.
- It benefits bioinformaticians with intermediate expertise.
- Local services are deployed at http://bioservices.sci.psu.ac.th for accessibility.
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