The comparative analysis of ss-rRNA sequences is one of the most powerful approaches for studying phylogenetic relationships among all organisms. Our ss-rRNA Taxonomy Assigning Pipeline (STAP) combines publicly available packages such as, PHYML, BLASTN, and CLUSTALW with our own automatic alignment masking and tree parsing programs. STAP makes automatic taxonomic assignments for ss-rRNAs based on neighbor-joining or maximum likelihood phylogenetic trees rather than on the top BLASTN hits, and thus its results are more reliable and accurate. Most importantly, the automation yields results comparable to those achievable by manual analysis, yet offers speed and capacity that are unattainable by manual efforts.
First, ss-rRNA sequences obtained either by PCR of environmental samples or by metagenomic shotgun sequencing are searched against our ss-rRNA database by BLASTN to select a related data set. STAP then automatically generates, masks, and trims the multiple sequence alignments. Next, it builds a phylogenetic tree by either the maximum likelihood or neighbor-joining method. Automated analysis of the tree yields taxonomic assignments for each query sequence.
A paper describing STAP has been published (7/2/08) in PLoS One.
• Wu D, Hartman A, Ward N, Eisen JA (2008) An Automated Phylogenetic Tree-Based Small Subunit rRNA Taxonomy and Alignment Pipeline (STAP). PLoS ONE 3(7): e2566. doi:10.1371/ journal.pone.0002566
There is only one file (STAP.zip) in this package, unzip it and the README.pdf file explains how to install STAP.