Table 4 Programs associated with the reciprocal smallest distance algorithm.

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.