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This paper describes a Taverna workflow environment with supporting web services for Single Nucleotide Polymorphisms (SNP) analysis of genes in shrimp. The workflow is used to investigate SNPs advantages for gene development. Our first workflow environment did not give satisfying results for the phylogenetic tree processes because the data flows between the web services would frequently time-out. Our solution employs local web service interfaces in a cluster, which Taverna accesses with the aid of Soaplab analysis tools. The cluster enables the modified workflow to rapidly process the large amount of sequenced data required by phylogenetic trees, and is highly reliable.