Thank you so much Chris! By "genome-wide", it is more like performing the same task (e.g. blast, clustalw and phyml) for every single gene in a genome. But because a single task could include +200 sequences to align or to build a phylogeny, it takes a significant amount of time and memory to process a single gene. So by using, for example, mpiblast and raxmlmpi, it could be possible to distribute these tasks over a cluster and finish an analysis in a reasonable time. I have googled and found these options Dell PowerEdge SC1435 (http://www.dell.com/content/products/productdetails.aspx/pedge_sc1435), Sun Fire X2100 M2 (http://www.sun.com/servers/entry/x2100/) and Mac Cluster (http://www.apple.com/science/solutions/workgroupcluster.html), do you have an experience with any of these options? Thanks again! Ahmed On 10/19/2007 9:16 AM, Ahmed Moustafa wrote: > Hello! > > What would be your recommendations for building a cluster of ~20-30 > machines with a budget of about $50K? > > I think more medium power machines would provide higher throughput > than fewer super power machines, especially, while performing > genome-wide analyses. > > What would you recommend for hardware brands and specs and OS? > > Thanks in advance!