I'm trying to identify the homologues of all genes between two fully assembled bacterial genomes (e.g. Bacillus subtilis and Staphylococcus aureus) in batch. It looks like relevant data are available on the NCBI COG database, but their 2012 COG software won't compile so I haven't been able to attempt this particular method. As an alternative to using this software, is there a flat file of gene name to COG (or equivalent) that I could just download then match in Excel? I greatly appreciate all suggestions. Thank you in advance!
Regarding the Cog Software: I downloaded the source code from ftp://ftp.ncbi.nih.gov/pub/wolf/COGs/COGsoft/ and I'm using Ubuntu 16.04 xenial.
g++ -O2 -c main.cpp
In file included from main.cpp:2:0:
os.h: In function ‘void myOpenDir(const char*)’:
os.h:13:16: error: ‘chdir’ was not declared in this scope
Makefile:9: recipe for target 'main.o' failed
make: * [main.o] Error 1