item:Protein_ML (molphy; max 40 species)
seqtype: A
itemmeta: L
itemmethod:(GEN_INFILE(in1);\
            cat infile |tr '?' '-' >in1.in;\
            mv in1.in infile;\
            RUN_IN_WINDOW((arb_protml $MODEL $SEARCH $REARRANGE $CALCLENGTH infile ;\
                           (test -f treefile && $DISPLAY_FUNC)));\
            RM_LOCAL_FILES(in1))&
itemhelp:protml.help

arg:DISPLAY_FUNC
argtype:choice_menu
arglabel:What to do with the tree?
argchoice:ARB ('tree_protml_'):arb_read_tree `/bin/cat arb_read_tree_args` tree_protml_$$ treefile "PRG=protml MODEL=$MODEL SEARCH=$SEARCH FILTER=$FILTER REARRANGE=$REARRANGE PKG=molphy"
argchoice:TextEdit:arb_textedit treefile &
argchoice:Treetool:treetool treefile

arg:MODEL
argtype:choice_menu
arglabel:Which model to use ?
argchoice:JTT:-j
argchoice:Dayhoff:-d
argchoice:mtREV24:-m
argchoice:Poisson:-p
argchoice:JTT-F:-jf
argchoice:Dayhoff-F:-df
argchoice:mtREV24-F:-mf
argchoice:Proportional:-pf

arg:SEARCH
argtype:choice_menu
arglabel:Search strategy
argchoice:Star decomposition:-s
argchoice:Exhaustive:-e
argchoice:Quick add:-q

arg:CALCLENGTH
argtype:choice_menu
arglabel:Calc branchlengths?
argchoice:Yes:1
argchoice:No:0

arg:REARRANGE
argtype:choice_menu
arglabel:Rearrangement
argchoice:None:0
argchoice:local Rearrangement search:-R
argchoice:LBP only:-RX

in:in1
informat:genbank
inmask:
insave: