Table 4

Programs associated with the reciprocal smallest distance algorithm.

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 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

Open Data