Motif Discovery at Whole Genome Level
Update 10-11-2005

Welcome to PhyloNet

Give it a try, tell you if you like it, don't like, how do
you want me to improve it, etc. I know there's still some
bugs, so check back for newer compiles.
Good luck and have a nice day!

  • Executable for linux: PhyloNet-v2b
  • Source Code: PhyloNet-v2b.tar.gz
  • README/help page: README
  • A "made-up" example: pnet_exp_1.tar.gz
    After untar the data, you should get 30 gene folders.
    Suppose this is what you see and you can try run with these options:
    (bifrost)[3:09pm]Exp1 277>>ls
    Gene1 Gene12 Gene15 Gene18 Gene20 Gene23 Gene26 Gene29 Gene4 Gene7 genelist
    Gene10 Gene13 Gene16 Gene19 Gene21 Gene24 Gene27 Gene3 Gene5 Gene8 alphabet
    Gene11 Gene14 Gene17 Gene2 Gene22 Gene25 Gene28 Gene30 Gene6 Gene9
    (bifrost)[3:09pm]Exp1 278>>PhyloNet-v2b -a alphabet -f Gene1/Gene1 -d genelist -id 10 -iq 10 -s4 -o2 > Gene1.pout

  • Output file: Gene1.pout
  • You also need wconsensus: wconsensus