5
itemmethod:( GEN_INFILE(in1); \
6
RUN_IN_WINDOW((arb_phyml infile DNA $MODEL $OPTFREQ $BASEFREQEST $TSTVRATIO $PINVAR $INTERACTIVE; \
13
arglabel:What to do with the tree?
14
argchoice:ARB ('tree_phyml_'):arb_read_tree `/bin/cat arb_read_tree_args` tree_phyml_$$ outtree "PRG=phyml FILTER=$FILTER STYPE=DNA"
15
argchoice:TextEdit:arb_textedit outfile &
16
argchoice:Treetool:treetool outtree
20
arglabel:Nuc. substitution model
32
arglabel:Optimize equilibrium freq.? [custom]
38
arglabel:Base frequency estimates
45
argchoice:fixed (4.00):0
50
arglabel:Proportion of invariable sites
51
argchoice:fixed (0.00):0
65
// --------------------------------------------------------------------------------
67
item:PHYML (Amino acids)
70
itemmethod:( GEN_INFILE(in1); \
71
RUN_IN_WINDOW((arb_phyml infile AA $MODEL $PINVAR $INTERACTIVE; \
78
arglabel:What to do with the tree?
79
argchoice:ARB ('tree_phyml_'):arb_read_tree `/bin/cat arb_read_tree_args` tree_phyml_$$ outtree "PRG=phyml FILTER=$FILTER STYPE=AA"
80
argchoice:TextEdit:arb_textedit outfile &
81
argchoice:Treetool:treetool outtree
85
arglabel:AA substitution model
99
arglabel:Proportion of invariable sites
100
argchoice:fixed (0.00):0
101
argchoice:estimated:1
105
arglabel:Interactive?
114
// --------------------------------------------------------------------------------
119
itemmethod:(GEN_INFILE(in1);\
4
itemmethod:(GOTO_LOCAL_DIR;GEN_PHYLIP(infile) && \
120
5
RUN_IN_WINDOW((arb_proml $BOOTSTRAP $MODEL $VIEWOUT $ANALYSIS $RANDOM $REARRANGE \
121
6
$RATE_VARIATION $VARIATION_COEFF $HMM_RATES $INV_FRACTION \
122
$INTERACTIVE; $DISPLAY_FUNC));\
123
RM_LOCAL_FILES(in1) )&
9
RM_LOCAL_FILES(TmpInputFile) )&
124
10
itemhelp:proml.help