#---------------- CODEML MENU ---------------------

item:Codeml
itemmethod: (readseq -a -f11 in1 | sed "s/YF//1" > in2; /home/tulio/testGDE/codemlmenu.pl in2 $outfile $phylotree $noisy $verbose $runmode $seqtype $CodonFreq $aaDist $aaRatefile $model $NSsites $icode $Mgene $fix_kappa $kappa $fix_omega $omega $fix_alpha $alpha $M $ncatG $fix_rho $rho $clock $getSE $RateAncestor .45e-6 $cleandata; xterm -e codeml method.ctl >& erros; emacs erros;)&

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:seqtype
arglabel:Seq. type
argtype:choice_menu
argchoice:codons:1
argchoice:AAs:2
argchoice:codons-->AAs:3

arg:CodonFreq
arglabel:Codon Frequence
argtype:choice_menu
argchoice:1/61 each:0
argchoice:F1X4:1
argchoice:F3X4:2
argchoice:codon table:3

arg:aaDist
arglabel:aaDist
argtype:choice_menu
argchoice:equal:0
argchoice:geometric:+
argchoice:linear:-

arg:aaRatefile 
arglabel:aaRatefile
argtype:choice_menu
argchoice:mtmam.dat:mtmam.dat
argchoice:dayhoff.dat:dayhoff.dat
argchoice:jones.dat:jones.dat

arg:model
arglabel:Model for codons
argtype:choice_menu
argchoice:one:0
argchoice:b:1
argchoice:2 or more dN/dS ratios for branches:2
arglabel:Model for AAs or codon-translated AAs
argchoice:poisson:0
argchoice:proportional:1
argchoice:Empirical:2
argchoice:Empirical+F:3
argchoice:FromCodon:6
argchoice:AAClasses:7
argchoice:REVaa_0:8
argchoice:REVaa(nr=189):9

arg:NSsites
arglabel:NSsites
argtype:choice_menu
argchoice:one w:0
argchoice:neutral:1
argchoice:positive:2
argchoice:discrete:3
argchoice:freqs:4
argchoice:gamma:5
argchoice:2gamma:6
argchoice:beta:7
argchoice:beta&w:8
argchoice:beta&gamma:9
argchoice:3normal:10

arg:icode
arglabel:icode
argtype:choice_menu
argchoice:standard genetic code:0
argchoice:mammalian mt:1
argchoice:yeast mt:2
argchoice:mold mt:3
argchoice:invertebrate mt:4
argchoice:ciliate nuclear:5
argchoice:echinoderm mt:6
argchoice:euplotid mt:7
argchoice:alternative yeast nu:8
argchoice:ascidian mt:9
argchoice:blepharisma nu:10

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:.3

arg:fix_omega
arglabel:fix_omega
argtype:choice_menu
argchoice:estimate:0
argchoice:omega or omega_1 fixed:1

arg:omega
arglabel:initial or fixed omega, for codons or codon-based AAs
argtype:slider
argmin:0
argmax:10
argvalue:1.3

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:3

arg:fix_rho
arglabel:fix_rho
argtype:choice_menu
argchoice:estimate rho (correlation parameter):0
argchoice:fix it at rho:1

arg:rho
arglabel:rho
argtype:choice_menu
argchoice:initial or fixed rho:0
argchoice:no correlation:0

arg:clock
arglabel:clock
argtype:choice_menu
argchoice:no clock, unrooted tree:0
argchoice:clock, rooted tree:1

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:cleandata
arglabel:remove sites with ambiguity data ?
argtype:choice_menu
argchoice:no:0
argchoice:yes:1



in:in1
informat:genbank
insave:
inmask: