| 1 | // this menu defines windows for two RAxml interfaces: DNA and PROTEIN |
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| 2 | // (depending on whether RAXML_DNA is defined or not) |
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| 3 | |
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| 4 | #define RAXML_CODE(_TYPE_,_PARAMS_) \ |
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| 5 | (GOTO_LOCAL_DIR ; \ |
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| 6 | arb_export_rates --arb-notify -r "$RATES" > weights && \ |
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| 7 | GEN_PHYLIP(infile) && \ |
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| 8 | RUN_IN_WINDOW(arb_raxml _TYPE_ infile weights "$BASETREE" $CONSTRAINT \ |
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| 9 | $RANDOMSTART $OPTIMIZEPARAMETERS $SEARCH \ |
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| 10 | "$INITIALREARRANGEMENT" "$SEED" \ |
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| 11 | "$NUMBEROFRUNS" "$TAKETREES" $CONSENSE \ |
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| 12 | "PRG=RAxML FILTER=$FILTER RATE=$RATES ALGO=!$SEARCH" \ |
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| 13 | _PARAMS_ \ |
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| 14 | ); \ |
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| 15 | RM_LOCAL_FILES(TmpInputFile last.infile treefile.in weights RAxML_info.treefile) )& |
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| 16 | |
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| 17 | #ifdef RAXML_DNA |
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| 18 | item:RAxML (DNA) |
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| 19 | itemmethod: RAXML_CODE(DNA,$RATEMODELNUC $NUMCATEGORIES) |
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| 20 | seqtype:N |
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| 21 | itemmeta:R |
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| 22 | #else |
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| 23 | item:RAxML (Protein) |
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| 24 | itemmethod: RAXML_CODE(PROTEIN,"$RATEMODELPROT" "$MATRIXNAME$EMPBFREQ") |
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| 25 | seqtype:A |
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| 26 | itemmeta:x |
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| 27 | #endif |
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| 28 | itemhelp:raxml.help |
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| 29 | |
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| 30 | arg:RATES |
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| 31 | argtype:weights |
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| 32 | arglabel:Select a Weighting Mask |
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| 33 | argchoice:POS_VAR_BY_PAR |
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| 34 | |
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| 35 | arg:BASETREE |
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| 36 | argtype:tree |
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| 37 | arglabel:Base tree |
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| 38 | argchoice:???? |
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| 39 | |
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| 40 | arg:CONSTRAINT |
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| 41 | argtype:choice_menu |
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| 42 | arglabel:Use as constraint tree |
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| 43 | argchoice:No:0 |
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| 44 | argchoice:Yes:1 |
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| 45 | |
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| 46 | arg:RANDOMSTART |
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| 47 | argtype:choice_menu |
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| 48 | arglabel:Generate random starting tree\n(if no tree selected) |
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| 49 | argchoice:No:0 |
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| 50 | argchoice:Yes:1 |
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| 51 | |
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| 52 | |
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| 53 | |
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| 54 | #ifdef RAXML_DNA |
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| 55 | |
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| 56 | arg:RATEMODELNUC |
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| 57 | argtype:choice_menu |
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| 58 | arglabel: Rate Distribution Model |
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| 59 | argchoice:GTRGAMMA:GTRGAMMA |
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| 60 | argchoice:GTRCAT:GTRCAT |
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| 61 | argchoice:GTRGAMMAI:GTRGAMMAI |
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| 62 | argchoice:GTRCATI:GTRCATI |
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| 63 | |
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| 64 | arg:NUMCATEGORIES |
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| 65 | argtype:text |
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| 66 | arglabel: No. rate categories (GTRCAT only) |
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| 67 | argtext:25 |
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| 68 | |
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| 69 | #else |
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| 70 | |
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| 71 | arg:RATEMODELPROT |
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| 72 | argtype:choice_menu |
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| 73 | arglabel:Rate Distribution Model |
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| 74 | argchoice:PROTGAMMA:PROTGAMMA |
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| 75 | argchoice:PROTCAT:PROTCAT |
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| 76 | argchoice:PROTGAMMAI:PROTGAMMAI |
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| 77 | argchoice:PROTCATI:PROTCATI |
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| 78 | |
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| 79 | arg:MATRIXNAME |
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| 80 | argtype:choice_menu |
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| 81 | arglabel:AA Substitution Model |
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| 82 | argchoice:DAYHOFF:DAYHOFF |
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| 83 | argchoice:DCMUT:DCMUT |
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| 84 | argchoice:JTT:JTT |
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| 85 | argchoice:MTREV:MTREV |
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| 86 | argchoice:WAG:WAG |
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| 87 | argchoice:RTREV:RTREV |
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| 88 | argchoice:CPREV:CPREV |
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| 89 | argchoice:VT:VT |
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| 90 | argchoice:BLOSUM62:BLOSUM62 |
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| 91 | argchoice:MTMAM:MTMAM |
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| 92 | argchoice:LG:LG |
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| 93 | argchoice:MTART:MTART |
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| 94 | argchoice:MTZOA:MTZOA |
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| 95 | argchoice:PMB:PMB |
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| 96 | argchoice:HIVB:HIVB |
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| 97 | argchoice:HIVW:HIVW |
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| 98 | argchoice:JTTDCMUT:JTTDCMUT |
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| 99 | argchoice:FLU:FLU |
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| 100 | argchoice:LG4M:LG4M |
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| 101 | argchoice:LG4X:LG4X |
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| 102 | argchoice:GTR:GTR |
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| 103 | argchoice:GTR_UNLINKED:GTR_UNLINKED |
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| 104 | argchoice:DUMMY:DUMMY |
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| 105 | argchoice:DUMMY2:DUMMY2 |
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| 106 | argchoice:AUTO:AUTO |
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| 107 | |
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| 108 | arg:EMPBFREQ |
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| 109 | arglabel:Use empirical base frequencies? |
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| 110 | argtype:choice_menu |
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| 111 | argchoice:No: |
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| 112 | argchoice:Yes:F |
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| 113 | |
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| 114 | #endif |
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| 115 | |
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| 116 | arg:OPTIMIZEPARAMETERS |
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| 117 | argtype:choice_menu |
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| 118 | #ifdef RAXML_DNA |
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| 119 | arglabel:Optimize branches/parameters\n(GTRGAMMA only) |
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| 120 | #else |
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| 121 | arglabel:Optimize branches/parameters\n(PROTGAMMA only) |
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| 122 | #endif |
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| 123 | argchoice:No:0 |
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| 124 | argchoice:Yes:1 |
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| 125 | |
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| 126 | arg:SEARCH |
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| 127 | argtype:choice_menu |
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| 128 | arglabel:Select RAxML algorithm |
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| 129 | argchoice:new rapid hill climbing:d |
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| 130 | argchoice:old hill climbing:o |
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| 131 | argchoice:optimize input tree:e |
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| 132 | argchoice:rapid bootstrap analysis:a |
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| 133 | argchoice:add new sequences to input tree (MP):p |
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| 134 | argchoice:randomized tree searches (fixed start tree):t |
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| 135 | |
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| 136 | arg:SEED |
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| 137 | argtype:text |
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| 138 | arglabel:Random seed\n(empty=use time) |
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| 139 | argtext: |
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| 140 | |
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| 141 | arg:INITIALREARRANGEMENT |
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| 142 | argtype:text |
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| 143 | arglabel:Initial rearrangement setting\n(empty=autodetect) |
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| 144 | argtext: |
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| 145 | |
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| 146 | arg:NUMBEROFRUNS |
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| 147 | argtype:text |
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| 148 | arglabel:Number of runs |
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| 149 | argtext:1 |
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| 150 | |
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| 151 | arg:TAKETREES |
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| 152 | argtype:text |
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| 153 | arglabel:Select ## best trees |
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| 154 | argtext:1 |
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| 155 | |
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| 156 | arg:CONSENSE |
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| 157 | argtype:choice_menu |
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| 158 | arglabel:What to do with selected trees? |
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| 159 | argchoice:Import into ARB:import |
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| 160 | argchoice:Create consensus tree:consense |
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| 161 | |
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| 162 | in:TmpInputFile |
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| 163 | informat:genbank |
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| 164 | insave: |
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| 165 | |
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