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Table 4 Programs associated with the reciprocal smallest distance algorithm.

From: Cloud computing for comparative genomics

Program name Description a module used by the main program which executes the RSD reciprocal smallest distance ortholog detection algorithm a suite of utilities, many of which wrap external programs such as clustalW and PAML a package used by the main program that builds all-against-all BLAST databases for fast execution of RSD
clustal2phylip a small perl function that converts clustalw alignment files into files that are recognized by paml
codeml.ctl_cp the control file required by RSD to properly calculate the maximum likelihood estimates of distance between two protein sequences an error reporter used by RSD the directive file used by RSD
examples a directory containing examples of inputs and outputs to and Blast_co
  1. These programs are required for running the RSD package on a cloud computing platform such as Amazon's Elastic MapReduce. These programs are packaged and available for download at and are also provided as additional files associated with the manuscript.