Integrated Automatic Workflow for Phylogenetic Tree Analysis Using Public Access and Local Web Services.

Integrated Automatic Workflow for Phylogenetic Tree Analysis Using Public Access and Local Web Services. J Integr Bioinform. 2016 Mar 01;13(1):7-22 Authors: Damkliang K, Tandayya P, Sangket U, Pasomsub E Abstract At the present, coding sequence (CDS) has been discovered and larger CDS is being revealed frequently. Approaches and related tools have also been developed and upgraded concurrently, especially for phylogenetic tree analysis. This paper proposes an integrated automatic Taverna workflow for the phylogenetic tree inferring analysis using public access web services at European Bioinformatics Institute (EMBL-EBI) and Swiss Institute of Bioinformatics (SIB), and our own deployed local web services. The workflow input is a set of CDS in the Fasta format. The workflow supports 1,000 to 20,000 numbers in bootstrapping replication. The workflow performs the tree inferring such as Parsimony (PARS), Distance Matrix - Neighbor Joining (DIST-NJ), and Maximum Likelihood (ML) algorithms of EMBOSS PHYLIPNEW package based on our proposed Multiple Sequence Alignment (MSA) similarity score. The local web services are implemented and deployed into two types using the Soaplab2 and Apache Axis2 deployment. There are SOAP and Java Web Service (JWS) providing WSDL endpoints to Taverna Workbench, a workflow manager. The workflow has been validated, the performance has been measured, and its results have been verified. Our workflow's execution time ...
Source: Journal of integrative bioinformatics - Category: Bioinformatics Tags: J Integr Bioinform Source Type: research