| 1 | // this menu defines windows for two RAxml interfaces: DNA and PROTEIN |
|---|
| 2 | // (depending on whether RAXML_DNA is defined or not) |
|---|
| 3 | |
|---|
| 4 | #define RAXML_CODE(_TYPE_,_PARAMS_) \ |
|---|
| 5 | (GOTO_LOCAL_DIR ; \ |
|---|
| 6 | arb_export_rates -r "$RATES" > weights; \ |
|---|
| 7 | arb_convert_aln -GenBank in1 -phylip2 infile; \ |
|---|
| 8 | RUN_IN_WINDOW(arb_raxml _TYPE_ infile weights "$TREE" $CONSTRAINT \ |
|---|
| 9 | $RANDOMSTART $OPTIMIZEPARAMETERS $SEARCH \ |
|---|
| 10 | "$INITIALREARRANGEMENT" "$SEED" \ |
|---|
| 11 | "$NUMBEROFRUNS" "$TAKETREES" $CONSENSE \ |
|---|
| 12 | _PARAMS_ \ |
|---|
| 13 | ); \ |
|---|
| 14 | RM_LOCAL_FILES(in1 last.infile treefile.in weights RAxML_info.treefile) )& |
|---|
| 15 | |
|---|
| 16 | #ifdef RAXML_DNA |
|---|
| 17 | item:RAxML (DNA) |
|---|
| 18 | itemmethod: RAXML_CODE(DNA,$RATEMODELNUC $NUMCATEGORIES) |
|---|
| 19 | seqtype:N |
|---|
| 20 | itemmeta:R |
|---|
| 21 | #else |
|---|
| 22 | item:RAxML (Protein) |
|---|
| 23 | itemmethod: RAXML_CODE(PROTEIN,"$RATEMODELPROT" "$MATRIXNAME$EMPBFREQ") |
|---|
| 24 | seqtype:A |
|---|
| 25 | itemmeta:P |
|---|
| 26 | #endif |
|---|
| 27 | itemhelp:raxml.help |
|---|
| 28 | |
|---|
| 29 | arg:RATES |
|---|
| 30 | argtype:weights |
|---|
| 31 | arglabel:Select a Weighting Mask |
|---|
| 32 | argchoice:POS_VAR_BY_PAR |
|---|
| 33 | |
|---|
| 34 | arg:TREE |
|---|
| 35 | argtype:tree |
|---|
| 36 | arglabel:Base tree |
|---|
| 37 | argchoice:???? |
|---|
| 38 | |
|---|
| 39 | arg:CONSTRAINT |
|---|
| 40 | argtype:choice_menu |
|---|
| 41 | arglabel:Use as constraint tree |
|---|
| 42 | argchoice:No:0 |
|---|
| 43 | argchoice:Yes:1 |
|---|
| 44 | |
|---|
| 45 | arg:RANDOMSTART |
|---|
| 46 | argtype:choice_menu |
|---|
| 47 | arglabel:Generate random starting tree\n(if no tree selected) |
|---|
| 48 | argchoice:No:0 |
|---|
| 49 | argchoice:Yes:1 |
|---|
| 50 | |
|---|
| 51 | |
|---|
| 52 | |
|---|
| 53 | #ifdef RAXML_DNA |
|---|
| 54 | |
|---|
| 55 | arg:RATEMODELNUC |
|---|
| 56 | argtype:choice_menu |
|---|
| 57 | arglabel: Rate Distribution Model |
|---|
| 58 | argchoice:GTRMIX:GTRMIX |
|---|
| 59 | argchoice:GTRGAMMA:GTRGAMMA |
|---|
| 60 | argchoice:GTRCAT:GTRCAT |
|---|
| 61 | argchoice:GTRCAT_GAMMA:GTRCAT_GAMMA |
|---|
| 62 | argchoice:GTRGAMMAI:GTRGAMMAI |
|---|
| 63 | argchoice:GTRMIXI:GTRMIXI |
|---|
| 64 | argchoice:GTRCAT_GAMMAI:GTRCAT_GAMMAI |
|---|
| 65 | |
|---|
| 66 | arg:NUMCATEGORIES |
|---|
| 67 | argtype:text |
|---|
| 68 | arglabel: # rate categories (GTRCAT only) |
|---|
| 69 | argtext:25 |
|---|
| 70 | |
|---|
| 71 | #else |
|---|
| 72 | |
|---|
| 73 | arg:RATEMODELPROT |
|---|
| 74 | argtype:choice_menu |
|---|
| 75 | arglabel:Rate Distribution Model |
|---|
| 76 | argchoice:PROTMIX:PROTMIX |
|---|
| 77 | argchoice:PROTGAMMA:PROTGAMMA |
|---|
| 78 | argchoice:PROTCAT:PROTCAT |
|---|
| 79 | argchoice:PROTCAT_GAMMA:PROTCAT_GAMMA |
|---|
| 80 | argchoice:PROTGAMMAI:PROTGAMMAI |
|---|
| 81 | argchoice:PROTMIXI:PROTMIXI |
|---|
| 82 | argchoice:PROTCAT_GAMMAI:PROTCAT_GAMMAI |
|---|
| 83 | |
|---|
| 84 | arg:MATRIXNAME |
|---|
| 85 | argtype:choice_menu |
|---|
| 86 | arglabel:AA Substitution Model |
|---|
| 87 | argchoice:DAYHOFF:DAYHOFF |
|---|
| 88 | argchoice:DCMUT:DCMUT |
|---|
| 89 | argchoice:JTT:JTT |
|---|
| 90 | argchoice:MTREV:MTREV |
|---|
| 91 | argchoice:WAG:WAG |
|---|
| 92 | argchoice:RTREV:RTREV |
|---|
| 93 | argchoice:CPREV:CPREV |
|---|
| 94 | argchoice:VT:VT |
|---|
| 95 | argchoice:BLOSUM62:BLOSUM62 |
|---|
| 96 | argchoice:MTMAM:MTMAM |
|---|
| 97 | argchoice:GTR:GTR |
|---|
| 98 | |
|---|
| 99 | arg:EMPBFREQ |
|---|
| 100 | arglabel:Use empirical base frequencies? |
|---|
| 101 | argtype:choice_menu |
|---|
| 102 | argchoice:No: |
|---|
| 103 | argchoice:Yes:F |
|---|
| 104 | |
|---|
| 105 | #endif |
|---|
| 106 | |
|---|
| 107 | arg:OPTIMIZEPARAMETERS |
|---|
| 108 | argtype:choice_menu |
|---|
| 109 | #ifdef RAXML_DNA |
|---|
| 110 | arglabel:Optimize branches/parameters\n(GTRMIX / GTRGAMMA only) |
|---|
| 111 | #else |
|---|
| 112 | arglabel:Optimize branches/parameters\n(PROTMIX / PROTGAMMA only) |
|---|
| 113 | #endif |
|---|
| 114 | argchoice:No:0 |
|---|
| 115 | argchoice:Yes:1 |
|---|
| 116 | |
|---|
| 117 | arg:SEARCH |
|---|
| 118 | argtype:choice_menu |
|---|
| 119 | arglabel:Select RAxML algorithm |
|---|
| 120 | argchoice:new rapid hill climbing:d |
|---|
| 121 | argchoice:old hill climbing:o |
|---|
| 122 | argchoice:optimize input tree:e |
|---|
| 123 | argchoice:rapid bootstrap analysis:a |
|---|
| 124 | argchoice:advanced bootstrap + refinement of BS tree:i |
|---|
| 125 | argchoice:add new sequences to input tree (MP):p |
|---|
| 126 | argchoice:randomized tree searches (fixed start tree):t |
|---|
| 127 | |
|---|
| 128 | // argchoice:optimize input tree (GAMMA/GAMMAI only):e |
|---|
| 129 | // argchoice:advanced bootstrap + refinement of BS tree (GAMMA):i |
|---|
| 130 | // argchoice:randomized tree searches on one fixed starting tree:t |
|---|
| 131 | |
|---|
| 132 | arg:SEED |
|---|
| 133 | argtype:text |
|---|
| 134 | arglabel:Random seed\n(empty=use time) |
|---|
| 135 | argtext: |
|---|
| 136 | |
|---|
| 137 | arg:INITIALREARRANGEMENT |
|---|
| 138 | argtype:text |
|---|
| 139 | arglabel:Initial rearrangement setting\n(empty=autodetect) |
|---|
| 140 | argtext: |
|---|
| 141 | |
|---|
| 142 | arg:NUMBEROFRUNS |
|---|
| 143 | argtype:text |
|---|
| 144 | arglabel:Number of runs |
|---|
| 145 | argtext:1 |
|---|
| 146 | |
|---|
| 147 | arg:TAKETREES |
|---|
| 148 | argtype:text |
|---|
| 149 | arglabel:Select ## best trees |
|---|
| 150 | argtext:1 |
|---|
| 151 | |
|---|
| 152 | arg:CONSENSE |
|---|
| 153 | argtype:choice_menu |
|---|
| 154 | arglabel:What to do with selected trees? |
|---|
| 155 | argchoice:Import into ARB:import |
|---|
| 156 | argchoice:Create consense tree:consense |
|---|
| 157 | |
|---|
| 158 | in:in1 |
|---|
| 159 | informat:genbank |
|---|
| 160 | inmask: |
|---|
| 161 | insave: |
|---|
| 162 | |
|---|
