# Geanfammer test directory README file


  To test geanfammer.pl   type:

  geanfammer.pl geanfammer_test_FASTA_DB.fa

The default is to run 'fasta' program which should be in your exe PATH in Linux.



  geanfammer.pl geanfammer_test_FASTA_DB.fa a=b

will run Blastpgp(PSI blast) if it is in the PATH.


  geanfammer.pl geanfammer_test_FASTA_DB.fa a=b e=0.0001

Will run Blastpgp (PSI blast) with step evalue threshold of 0.0001



jong@salt2.med.harvard.edu