#---------------- Baseml MENU -------------------------
item:-----------PAML------------------

item:Baseml
itemmethod: (readseq -a -f11 in1 | sed "s/YF//1" > in2; /home/tulio/testGDE/basemlmenu.pl in2 $outfile $phylotree $noisy $verbose $runmode $model $Mgene $fix_kappa $kappa $fix_alpha $alpha $M $ncatG $nhomo $clock $getSE $RateAncestor .1e-6 $method; xterm -e baseml method.ctl)&

arg:outfile
arglabel:outfile name ?
argtype:text

arg:phylotree
arglabel:tree_file ?
argtype:text

arg:noisy
arglabel:how much rubbish on the screen
argtype:choice_menu
argchoice:1:1
argchoice:2:2
argchoice:3:3
argchoice:9:9

arg:verbose
arglabel:Output
argtype:choice_menu
argchoice:detailed output:1
argchoice:concise output:2


arg:runmode
arglabel:runmode
argtype:choice_menu
argchoice:usertree:0
argchoice:semi-automatic:1
argchoice:automatic:2
argchoice:StepwiseAddition:3
argchoice:PerturbationNNI:4
argchoice:pairwise:-2


arg:model
arglabel:Model for codons
argtype:choice_menu
argchoice:JC69:0
argchoice:K80:1
argchoice:F81:2
argchoice:F84:3
argchoice:HKY85:4
argchoice:TN93:5
argchoice:REV:6

arg:Mgene
arglabel:Mgene
argtype:choice_menu
argchoice:rates:0
argchoice:separate:1
argchoice:pi:2 
argchoice:kappa:3
argchoice:all:4

arg:fix_kappa
arglabel:fix_kappa
argtype:choice_menu
argchoice:kappa to be estimated:0
argchoice:kappa fixed:1

arg:kappa
arglabel:kappa
argtype:slider
argmin:0
argmax:10
argvalue:2.4


arg:fix_alpha
arglabel:fix_alpha
argtype:choice_menu
argchoice:estimate gamma shape parameter:0
argchoice:fix it at alpha:1

arg:alpha
arglabel:alpha 0 infinity (constant rate)
argtype:slider
argmin:0
argmax:10
argvalue:5

arg:M
arglabel:Malpha
argtype:choice_menu
argchoice:0:0
argchoice:1:1

arg:ncatG
arglabel:number of categories in the dG or AdG models of rates
argtype:slider
argmin:0
argmax:12
argvalue:8

arg:clock
arglabel:clock
argtype:choice_menu
argchoice:no clock, unrooted tree:0
argchoice:clock, rooted tree:1
argchoice:local clock:2
argchoice:TipDate:3

arg:nhomo
arglabel:nhomo
argtype:choice_list
argchoice:homogeneous:0
argchoice:kappa for branches:2
argchoice:N1:3
argchoice:N2don't want them:4


arg:getSE
arglabel:getSE
argtype:choice_menu
argchoice: don't want them:0
argchoice:want S.E.s of estimates:1

arg:RateAncestor
arglabel:RateAncestor
argtype:choice_menu
argchoice:rates (alpha >0):0
argchoice:ancestor states:1
argchoice:ancestor states 2:2

arg:method
arglabel:method
argtype:chooser
argchoice:simultaneous:0
argchoice:one branch at a time:1

in:in1
informat:genbank
inmask:
insave: