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