Table 4

Programs associated with the reciprocal smallest distance algorithm.

Program name


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


a small perl function that converts clustalw alignment files into files that are recognized by paml


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


a directory containing examples of inputs and outputs to and Blast_co

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 webcite and are also provided as additional files associated with the manuscript.

Wall et al. BMC Bioinformatics 2010 11:259   doi:10.1186/1471-2105-11-259

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