#---------Made by Eric W. Linton 1996 rev. 1997, 1999 and 2003----------#

#                   INTALLATION INSTRUCTIONS
# 1) Make sure you have the most current version of PAUP*4.0 and name it "paup". For Mr. Bayes
#    make sure the program is named mb. For Modeltest it should be called modeltest.
#    The name must be in all lowercase with no * or number extensions. 
# 2) Place all the programs in the GDE/bin/ folder including the modelblock3.1 file.
# 3) Login as superuser so that you can modify the main .GDEmenus file. If you modify
#    this file then these programs will be available to all individual accounts on the Unix
#    machine. If you only want these menus available for a specific user then place a
#    copy of .GDEmeus in that users home directory, then changes made will ONLY be 
#    available to that user account.
# 4) Copy and past into .GDEmenus file BELOW the heading menu:Phylogeny
# 5) Make sure that the itemmethod: line for each item is ONE line with NO returns.
# 6) Save changes and open GDE, check the Phylogeny menu
# 6) GO TO PAUP* Instructions... FIRST.

item:Modeltest3.06
itemmethod:(readseq -a -f17 in1 > .modeltest.in;  cat .modeltest.in /usr/local/biotools/GDE/bin/modelblock3.1 > .modeltest2.in; mkdir $MKD; mv -f .modeltest2.in $MKD/$FLN_MT.nex; /bin/rm -f gde*_*; cd $MKD/; xterm -e paup $FLN_MT.nex; modeltest < model.scores > $FLN_MT.results; mv model.scores $FLN_MT.scores; mv modelfit.log $FLN_MT.log; textedit $FLN_MT.results; )&
itemhelp:modeltest.help

in:in1
informat:genbank
insave:
inmask:

arg:MKD
arglabel:Project Directory (NO SPACES USE _ or -)
argtype:text

arg:FLN
arglabel:Filename:(_MT.nex automatically added)
argtype:text

arg:INFORMATION
arglabel:INSTRUCTIONS
argtype:choice_list
argchoice:Fill-in the Project Directory and Filename
argchoice:Have the taxa and mask you want to analyse chosen then click OK.
argchoice:Paup will run, then modeltest, then the results will appear.
argchoice:Now use the results to set-up Max Like using the normal Paup menus.
argchoice:REMEMBER unless the model is JC, K2P, F81, F84 or HKY USE the GTR model.

item:________________________
itemmethod: