source: tags/old_import_filter/GDEHELP/MENUS/phylip_ml.menu

Last change on this file was 5077, checked in by westram, 16 years ago
  • typo
  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date Id Revision
File size: 4.4 KB
Line 
1
2item:PHYML (DNA)
3seqtype: N
4itemmeta: D
5itemmethod:( GEN_INFILE(in1); \
6             RUN_IN_WINDOW((arb_phyml infile DNA $MODEL $OPTFREQ $BASEFREQEST $TSTVRATIO $PINVAR $INTERACTIVE; \
7                            $DISPLAY_FUNC )); \
8           )&
9itemhelp:phyml.help
10
11arg:DISPLAY_FUNC
12argtype:choice_menu
13arglabel:What to do with the tree?
14argchoice:ARB ('tree_phyml_'):arb_read_tree `/bin/cat arb_read_tree_args` tree_phyml_$$ outtree "PRG=phyml FILTER=$FILTER STYPE=DNA"
15argchoice:TextEdit:arb_textedit outfile &
16argchoice:Treetool:treetool outtree
17
18arg:MODEL
19argtype:choice_menu
20arglabel:Nuc. substitution model
21argchoice:HKY:0
22argchoice:F84:1
23argchoice:TN93:2
24argchoice:GTR:3
25argchoice:custom:4
26argchoice:JC69:5
27argchoice:KP2:6
28argchoice:F81:7
29
30arg:OPTFREQ
31argtype:choice_menu
32arglabel:Optimize equilibrium freq.? [custom]
33argchoice:No:0
34argchoice:Yes:1
35
36arg:BASEFREQEST
37argtype:choice_menu
38arglabel:Base frequency estimates
39argchoice:empirical:0
40argchoice:ML:1
41
42arg:TSTVRATIO
43argtype:choice_menu
44arglabel:Ts/tv ratio
45argchoice:fixed (4.00):0
46argchoice:estimated:1
47
48arg:PINVAR
49argtype:choice_menu
50arglabel:Proportion of invariable sites
51argchoice:fixed (0.00):0
52argchoice:estimated:1
53
54arg:INTERACTIVE
55argtype:choice_menu
56arglabel:Interactive?
57argchoice:No:0
58argchoice:Yes:1
59
60in:in1
61informat:genbank
62inmask:
63insave:
64
65// --------------------------------------------------------------------------------
66
67item:PHYML (Amino acids)
68seqtype: A
69itemmeta: M
70itemmethod:( GEN_INFILE(in1); \
71             RUN_IN_WINDOW((arb_phyml infile AA $MODEL $PINVAR $INTERACTIVE; \
72                            $DISPLAY_FUNC )); \
73           )&
74itemhelp:phyml.help
75
76arg:DISPLAY_FUNC
77argtype:choice_menu
78arglabel:What to do with the tree?
79argchoice:ARB ('tree_phyml_'):arb_read_tree `/bin/cat arb_read_tree_args` tree_phyml_$$ outtree "PRG=phyml FILTER=$FILTER STYPE=AA"
80argchoice:TextEdit:arb_textedit outfile &
81argchoice:Treetool:treetool outtree
82
83arg:MODEL
84argtype:choice_menu
85arglabel:AA substitution model
86argchoice:JTT:0
87argchoice:MtRev:1
88argchoice:WAG:2
89argchoice:DCMut:3
90argchoice:RtREV:4
91argchoice:CpREV:5
92argchoice:VT:6
93argchoice:Blosum62:7
94argchoice:MtMam:8
95argchoice:Dayhoff:9
96
97arg:PINVAR
98argtype:choice_menu
99arglabel:Proportion of invariable sites
100argchoice:fixed (0.00):0
101argchoice:estimated:1
102
103arg:INTERACTIVE
104argtype:choice_menu
105arglabel:Interactive?
106argchoice:No:0
107argchoice:Yes:1
108
109in:in1
110informat:genbank
111inmask:
112insave:
113
114// --------------------------------------------------------------------------------
115
116item:Phylip PROML
117seqtype: A
118itemmeta: O
119itemmethod:(GEN_INFILE(in1);\
120            RUN_IN_WINDOW((arb_proml $BOOTSTRAP $MODEL $VIEWOUT $ANALYSIS $RANDOM $REARRANGE \
121                                     $RATE_VARIATION $VARIATION_COEFF $HMM_RATES $INV_FRACTION \
122                                     $INTERACTIVE; $DISPLAY_FUNC));\
123            RM_LOCAL_FILES(in1) )&
124itemhelp:proml.help
125
126arg:DISPLAY_FUNC
127argtype:choice_menu
128arglabel:What to do with the tree?
129argchoice:ARB ('tree_proml_'):arb_read_tree `/bin/cat arb_read_tree_args` tree_proml_$$ outtree "PRG=proml FILTER=$FILTER PKG=phylip BOOT=$BOOTSTRAP MODEL=$MODEL ANALYSIS=$ANALYSIS"
130argchoice:TextEdit:arb_textedit outfile &
131argchoice:Treetool:treetool outtree
132
133arg:MODEL
134argtype:choice_menu
135arglabel:Model
136argchoice:Jones-Taylor-Thornton:JTT
137argchoice:Dayhoff PAM:PAM
138
139arg:ANALYSIS
140argtype:choice_menu
141arglabel:Analysis
142argchoice:Rough & fast:rough
143argchoice:Fine & slow:fine
144
145arg:REARRANGE
146argtype:choice_menu
147arglabel:Global rearrangements
148argchoice:No:0
149argchoice:Yes:1
150
151arg:RANDOM
152argtype:choice_menu
153arglabel:Randomize sequence order
154argchoice:Yes:1
155argchoice:No:0
156
157arg:RATE_VARIATION
158argtype:choice_menu
159arglabel:Rate variation among sites?
160argchoice:Constant rate of change:0
161argchoice:Gamma distributed rates:1
162argchoice:Gamma+Invariant sites:2
163
164arg:VARIATION_COEFF
165argtype:text
166arglabel:Variation coeff. (gamma only)
167argtext:4
168
169arg:HMM_RATES
170argtype:text
171arglabel:Rates in HMM (gamma only)
172argtext:4
173
174arg:INV_FRACTION
175argtype:text
176arglabel:Fraction of invariant sites
177argtext:0.1
178
179arg:BOOTSTRAP
180argtype:choice_menu
181arglabel:How many bootstraps ?
182argchoice:Do not bootstrap:0
183argchoice:10:10
184argchoice:100:100
185argchoice:500:500
186argchoice:1000:1000
187argchoice:5000:5000
188argchoice:10000:10000
189
190arg:VIEWOUT
191argtype:choice_menu
192arglabel:View report
193argchoice:No:0
194argchoice:Yes:1
195
196arg:INTERACTIVE
197argtype:choice_menu
198arglabel:Interactive? (no for bootstrap)
199argchoice:No:0
200argchoice:Yes:1
201
202in:in1
203informat:genbank
204inmask:
205insave:
206
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