| 1 | item:Phylip Distance Methods (Simple GUI Based Interface) |
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| 2 | itemmeta: G |
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| 3 | seqtype:* |
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| 4 | itemmethod:(GOTO_LOCAL_DIR;GEN_PHYLIP(infile) && \ |
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| 5 | RUN_IN_WINDOW(($CORRECTION_PROT;$CORRECTION_DNA;$PROGRAM_SEL;\ |
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| 6 | $DPGM;\ |
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| 7 | mv infile infile.1; \ |
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| 8 | mv -f outfile infile;\ |
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| 9 | (arb_echo $PROGRAM_FLAGS |$PROGRAM || STOP_ON_FAILURE($PROGRAM)) && \ |
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| 10 | $DISPLAY_FUNC));\ |
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| 11 | RM_LOCAL_FILES(TmpInputFile infile.1))& |
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| 12 | itemhelp:phylip_distance.help |
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| 13 | |
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| 14 | arg:DISPLAY_FUNC |
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| 15 | argtype:choice_menu |
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| 16 | arglabel:What to do with the tree? |
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| 17 | argchoice:ARB ('tree_ph_'):($CORRECTION_PROT;$CORRECTION_DNA;$PROGRAM_SEL;echo||$DPGM;arb_read_tree tree_ph_$$ outtree "PRG=$PROGRAM_NAME CORR=$TEXT FILTER=$FILTER PKG=phylip") |
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| 18 | argchoice:TextEdit:arb_textedit outfile |
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| 19 | argchoice:Treetool:treetool outtree |
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| 20 | |
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| 21 | arg:PROGRAM_SEL |
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| 22 | arglabel:Which method? |
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| 23 | argtype:choice_menu |
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| 24 | argchoice:Neighbor: PROGRAM=neighbor; PROGRAM_FLAGS="y"; PROGRAM_NAME=neighbor |
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| 25 | argchoice:UPGMA: PROGRAM=neighbor; PROGRAM_FLAGS="n y"; PROGRAM_NAME=UPGMA |
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| 26 | argchoice:Fitch: PROGRAM=fitch; PROGRAM_FLAGS="y"; PROGRAM_NAME=fitch |
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| 27 | argchoice:Kitsch: PROGRAM=kitsch; PROGRAM_FLAGS="y"; PROGRAM_NAME=kitsch |
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| 28 | |
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| 29 | arg:DPGM |
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| 30 | arglabel:Treat data as.. |
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| 31 | argtype:choice_menu |
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| 32 | argchoice:DNA/RNA:(arb_echo $DNAFLAGS |dnadist);TEXT=$DNATEXT |
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| 33 | argchoice:AA:(arb_echo $PROFLAGS |protdist);TEXT=$PROTEXT |
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| 34 | |
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| 35 | arg:CORRECTION_DNA |
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| 36 | arglabel:Correction (DNA) |
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| 37 | argtype:choice_menu |
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| 38 | argchoice:F84: DNATEXT=F84; DNAFLAGS="y" |
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| 39 | argchoice:Kimura 2-parameter: DNATEXT=Kimura; DNAFLAGS="d y" |
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| 40 | argchoice:Jukes-Cantor: DNATEXT=Jukes-Cantor; DNAFLAGS="d d y" |
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| 41 | // the following options cause crash with all distance programs: |
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| 42 | // argchoice:LogDet: DNATEXT=LogDet; DNAFLAGS="d d d y" |
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| 43 | // argchoice:Manual: DNATEXT=User; DNAFLAGS="" |
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| 44 | |
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| 45 | arg:CORRECTION_PROT |
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| 46 | arglabel:Correction (PROT) |
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| 47 | argtype:choice_menu |
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| 48 | argchoice:Jones-Taylor-Thornton: PROTEXT=JTT; PROFLAGS="y" |
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| 49 | argchoice:Dayhoff PAM matrix: PROTEXT=Dayhoff; PROFLAGS="p y" |
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| 50 | argchoice:Kimura formula: PROTEXT=Kimura; PROFLAGS="p p y" |
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| 51 | argchoice:Manual: PROTEXT=User; PROFLAGS="" |
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| 52 | |
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| 53 | in:TmpInputFile |
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| 54 | informat:genbank |
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| 55 | insave: |
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| 56 | |
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| 57 | // -------------------------------------------------------------------------------- |
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| 58 | |
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| 59 | item:Phylip Distance Matrix |
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| 60 | itemmeta: M |
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| 61 | seqtype:* |
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| 62 | itemmethod: GOTO_LOCAL_DIR;GEN_PHYLIP(infile) && \ |
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| 63 | RUN_IN_WINDOW(( $PREEDIT \ |
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| 64 | $DPGM ; \ |
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| 65 | arb_textedit outfile)) ; \ |
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| 66 | RM_LOCAL_FILES(TmpInputFile) |
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| 67 | itemhelp:phylip_distance.help |
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| 68 | |
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| 69 | arg:DPGM |
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| 70 | arglabel:Treat data as.. |
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| 71 | argtype:choice_menu |
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| 72 | argchoice:DNA/RNA:dnadist |
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| 73 | argchoice:AA:protdist |
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| 74 | |
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| 75 | arg:PREEDIT |
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| 76 | argtype:choice_menu |
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| 77 | arglabel:Edit input before running? |
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| 78 | argchoice:No: |
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| 79 | argchoice:Yes:arb_textedit infile ; echo "Press RETURN to start $DPGM" ; arb_wait > /dev/null ; |
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| 80 | |
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| 81 | in:TmpInputFile |
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| 82 | informat:genbank |
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| 83 | insave: |
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| 84 | |
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by 