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Table 4 Programs associated with the reciprocal smallest distance algorithm.

From: Cloud computing for comparative genomics

Program name Description
ReadFasta.py a module used by RSD.py
RSD.py the main program which executes the RSD reciprocal smallest distance ortholog detection algorithm
BioUtilities.py a suite of utilities, many of which wrap external programs such as clustalW and PAML
Utility.py a package used by BioUtilities.py
Blast_compute.py 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
execute.py an error reporter used by RSD
RSD_common.py the directive file used by RSD
examples a directory containing examples of inputs and outputs to RSD.py and Blast_co mpute.py.
  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 http://roundup.hms.harvard.edu and are also provided as additional files associated with the manuscript.