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Project Progress

64 completed eukaryotic genomes were retrieved from the appropriate sequencing centers. Homologous sequences to every predicted Trichoplax adhaerens gene were identified using the BLASTP algorithm (Altschul et al, 1997). From the multiple BLASTP searches, gene families with more than one representative from any genome were discarded and those remaining families with a minimum of four sequences were selected for phylogenetic reconstruction. This conservative approach was used to minimize the inadvertent analysis of paralogs. The sequences were aligned and the optimal protein models of sequence substitution and estimated parameters for each gene family were calculated. According to the selected parameters, hypotheses of relationships were re-constructed using Maximum Likelihood to construct source trees. The supertree software CLANN was then used to find the D-fit supertree that best described the relationships from all the source trees. Currently we are running analyses to assess the support for the reconstructed phylogeny.