--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/orthologs/ucsb_hamster/lib/wisecfg/wise.per	Tue Mar 11 12:19:13 2014 -0700
@@ -0,0 +1,104 @@
+! this is the wise config file
+! for you to fool around with Remember ! lines are comments
+! and keys should go flush with the left hand margin
+!
+! All wise.cfg's at the moment should have interactive key
+!
+interactive
+!
+! This is the linkfile designation (for searchwise/swise)
+!
+linkfile wise.links
+!
+! The next lines show a UNIX style background system
+!
+queuecommand nice nohup csh
+addamperstand
+!
+!
+viewlength 20
+!
+! view command for pairwise....
+viewer more
+!
+!viewbackground
+!
+!
+!The next two keys give default codon and matrix files
+!I'm using here the fact that pairwise/searchwise will open files
+!from WISECONFIGDIR if it can't open the file as the straight filename
+!
+codondefault      codon.table
+matrixdefault     blosum62.bla
+!
+!
+! The next lines give default for all situations gap and ext
+! and other parameters
+!
+gapdefault 1900
+extdefault 200
+framedefault 2500
+frameextdefault 2000
+stopdefault 500
+!
+!The next lines gives default specific for profiles or protein sequences
+!I've found these values by rule of thumb. These values will superceed
+! the defaults above
+!
+gap_pro 2200
+ext_pro 200
+gap_seq 700
+ext_seq 70
+!
+!This gives the number of cells to report in PairWise
+!
+reportrate 10000
+!
+!This tells the screen length in PairWise/Opensearch help files
+!
+screenlength 20
+!
+!These give help files
+!
+localhtmlhelp http://www.sanger.ac.uk/~birney/wise/help/
+!
+! This gives the SRS link and library links
+!
+srslink     http://www.sanger.ac.uk/srs/srsc?
+srslibrary  +-l+swissprot+-l+embl+-l+swissnew+-l+emnew
+!
+! This gives the sort of extensions to append to output file
+! in searchwise
+!
+outputappend     .out
+htmlappend       .html
+alignhtmlappend  _aln.html
+alignappend      .aln
+!
+pairmainhelp      pairmain.hlp
+pairalignhelp     pairaln.hlp
+confighelp        pairconfig.hlp
+!
+protopmenuhelp    buildprofile.hlp
+promatrixmenuhelp     pwmatrix.hlp 
+proweightmenuhelp  pwweights.hlp
+progapmenuhelp    pwgap.hlp
+!
+searchmainhelp    searchmain.hlp
+searchparahelp    searchaln.hlp
+searchsubmithelp  searchsubmit.hlp
+!
+!
+!
+stagger   500
+highscore 250
+align      50
+!
+deletecom
+!
+!
+!
+hard_linkage
+
+
+