#----------------------- Lamarc (Alpha 01/2002 version) -------------------
item:Lamarc (Alpha Version) XML converter
itemmethod:( readseq -a -f11 in1 > in2; (echo 1; echo $regionname; echo $popname; echo n; echo in2; echo $another; echo $lamarcfile) | converter)&

arg:regionname
arglabel:region name
argtype:text

arg:popname
arglabel:population name
argtype:text

arg:lamarcfile
arglabel:filename
argtype:text

arg:another
arglabel:another file ?
argtype:chooser
argchoice:yes:y; echo 1; echo $regionname2; echo $popname2; echo n; echo $fileadd; echo $insert2
argchoice:no:n

arg:fileadd
arglabel:file to add
argtype:text

arg:regionname2
arglabel:region name
argtype:text

arg:popname2
arglabel:population name
argtype:text

arg:insert2
arglabel:another file ?
argtype:chooser
argchoice:yes:y ; echo 1; echo $regionname3; echo $popname3; echo n; echo $fileadd3; echo n
argchoice:no:n

arg:fileadd3
arglabel:file to add
argtype:text

arg:regionname3
arglabel:region name
argtype:text

arg:popname3
arglabel:population name
argtype:text



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inmask:

item:ALPHA-LAMARC
itemmethod:((echo $filename ; echo $datamodel; echo $transition; echo $basefreq; echo $ratescategories; echo $effectivepopsize; echo G )| lamarc)&

arg:filename
arglabel:filename in XML format
argtype:text

arg:datamodel
arglabel:Data model
argtype:chooser
argchoice:F84:D; echo 1; echo 1; echo F; echo Y; echo Y

arg:transition
arglabel:transition/transversion
argtype:chooser
argchoice:2.0 (default):
argchoice:Enter value: D; echo 1; echo 2; echo $transvalue; echo Y; echo Y

arg:transvalue
arglabel:transition/transvertion value
argtype:text

arg:basefreq
arglabel:Base frequence
argtype:chooser
argchoice:25% each base (default):
argchoice:Enter value: D; echo 1; echo 3; echo $basevalue; echo Y; echo Y

arg:basevalue
arglabel:Base frequence values (A C G T) separate by spaces
argtype:text


arg:ratescategories
arglabel:Rate Categories and Probabilities
argtype:chooser
argchoice:one category (default):
argchoice:more than one category:D; echo 1; echo 4; echo $howmanycategories; echo $ratesnumber ; echo $ratesfrequence; echo $ratescorrelation; echo Y; echo Y

arg:howmanycategories
arglabel:How many categories
argtype:text

arg:ratesnumber
arglabel:Enter the rates for the categories (default 1 1)
argtype:text

arg:ratesfrequence
arglabel:Enter the frequencies for the categories (scaled to add to 1.0)
argtype:text

arg:ratescorrelation
arglabel:Enter the Correlation among sites
argtype:text

arg:effectivepopsize
arglabel:Evolutionary Forces: Effective population size
argtype:chooser
argchoice:Use WATTERSON's estimator for Theta values:
argchoice:Change Theta:E ; echo 1; echo $thetavalue; echo Y; echo Y

arg:thetavalue
arglabel:Enter theta value for population (default 0.102231) 
argtype:text 

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