Table 4.
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. |
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.