# ALIGN


#ALIGN.matrix_=BL50
#ALIGN.linlen_=60



# CLUSTALW_PROFILE


#CLUSTALW_PROFILE.actions_=-profile
#CLUSTALW_PROFILE.phylip_alig_=0
#CLUSTALW_PROFILE.quicktree_=slow
#CLUSTALW_PROFILE.matrix_=gonnet
#CLUSTALW_PROFILE.dnamatrix_=iub
#CLUSTALW_PROFILE.gapopen_=10
#CLUSTALW_PROFILE.gapext_=0.20
#CLUSTALW_PROFILE.endgaps_=1
#CLUSTALW_PROFILE.gapdist_=8
#CLUSTALW_PROFILE.pgap_=1
#CLUSTALW_PROFILE.hgap_=1
#CLUSTALW_PROFILE.maxdiv_=30
#CLUSTALW_PROFILE.negative_=0
#CLUSTALW_PROFILE.transweight_=0.5
#CLUSTALW_PROFILE.ktuple_=1
#CLUSTALW_PROFILE.topdiags_=5
#CLUSTALW_PROFILE.window_=5
#CLUSTALW_PROFILE.pairgap_=3.00
#CLUSTALW_PROFILE.pwmatrix_=gonnet
#CLUSTALW_PROFILE.pwdnamatrix_=iub
#CLUSTALW_PROFILE.pwgapopen_=10.00
#CLUSTALW_PROFILE.pwgapext_=0.10
#CLUSTALW_PROFILE.kimura_=0
#CLUSTALW_PROFILE.tossgaps_=0
#CLUSTALW_PROFILE.bootstrap_=1000
#CLUSTALW_PROFILE.bootlabels_=node
#CLUSTALW_PROFILE.outputtree_=PHYLIP
#CLUSTALW_PROFILE.output_=outfile.aln
#CLUSTALW_PROFILE.outorder_=aligned
#CLUSTALW_PROFILE.seqnos_=0
#CLUSTALW_PROFILE.nosecstr1_=1
#CLUSTALW_PROFILE.nosecstr2_=1
#CLUSTALW_PROFILE.helixgap_=4
#CLUSTALW_PROFILE.strandgap_=4
#CLUSTALW_PROFILE.loopgap_=1
#CLUSTALW_PROFILE.terminalgap_=2
#CLUSTALW_PROFILE.helixendin_=3
#CLUSTALW_PROFILE.helixendout_=0
#CLUSTALW_PROFILE.strandendin_=1
#CLUSTALW_PROFILE.strandendout_=1
#CLUSTALW_PROFILE.secstrout_=STRUCTURE

#CLUSTALW_PROFILE.score_=percent
#CLUSTALW_PROFILE.gde_lower_=0
#CLUSTALW_PROFILE.seed_=0
#CLUSTALW_PROFILE.typeseq_=DNA



# FINGERPRINTSCAN


#FINGERPRINTSCAN.graph_scan_=0
#FINGERPRINTSCAN.number_bits_=
#FINGERPRINTSCAN.random_shuffle_=0
#FINGERPRINTSCAN.profile_score_=15



# HMMPFAM


#HMMPFAM.HMMDB_=Pfam-A.full
#HMMPFAM.E_value_cutoff_=10.0



# MSA


#MSA.optimal_=0
#MSA.endgap_=0
#MSA.unweight_=0





# PFTOOLS


PFTOOLS.pftools_=pfscan
PFTOOLS.prosite_=1
PFTOOLS.gcg2psa_=1
PFTOOLS.aa_or_nuc_db_=protein
PFTOOLS.aadb_=UNIPROT
PFTOOLS.nucdb_=genbank
PFTOOLS.psa2msa_=1





# PRIMERS


#PRIMERS.minsize_=18
#PRIMERS.maxsize_=27
#PRIMERS.maxdifftm_=100.0
#PRIMERS.explainflag_=0
#PRIMERS.numreturn_=5
#PRIMERS.outfile_=outfile.out


# SAPS


#SAPS.documented_=0
#SAPS.terse_=0
#SAPS.verbose_=0
#SAPS.table_=0
#SAPS.specie_=MOUSE
#SAPS.H_positive_=0





#