| 1 | # Menu for RAxML 8 |
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| 2 | # |
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| 3 | # User documentation in ../../GDEHELP/HELP_WRITTEN/raxml8.help |
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| 4 | # |
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| 5 | # use cases: |
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| 6 | # |
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| 7 | # - build small publication dna tree |
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| 8 | # - multiple ml searches, pick best |
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| 9 | # - run bootstraps |
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| 10 | # - import best ml tree + support values |
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| 11 | # - import consensus from bootstraps |
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| 12 | # |
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| 13 | # - build quick&dirty dna tree (or large tree) |
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| 14 | # - fast bootstraps |
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| 15 | # - import consensus |
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| 16 | # |
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| 17 | # - score given tree (=calculate likelihood) |
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| 18 | # - calc branchlens of given tree (+calculate likelihood) into new tree |
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| 19 | # - optimize given tree into new tree |
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| 20 | # - extend tree (=add species missing in tree; keep topology) |
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| 21 | # - calculate bootstrap values for existing tree |
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| 22 | # |
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| 23 | # @@@ possible use cases: |
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| 24 | # - build AA tree |
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| 25 | # - get support SH-like support values for tree |
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| 26 | |
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| 27 | menu:Phylogeny max. Likelihood |
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| 28 | |
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| 29 | item:RAxML 8 (DNA) |
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| 30 | itemmethod: ${ARB_XCMD} arb_raxml8.sh -p $PROTOCOL -fi "$FILTER" -it "$INPUTTREE" -m $MODEL -s "$SEED" -b $BOOTSTRAPS -r $REPEATS -nt -t "$THREADS" -f INPUTFILE -n $TREENAME $MRETREE & |
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| 31 | itemhelp:raxml8.help |
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| 32 | itemmeta:8 |
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| 33 | seqtype:N |
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| 34 | |
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| 35 | in:INPUTFILE |
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| 36 | informat:genbank |
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| 37 | insave: |
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| 38 | |
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| 39 | arg:INPUTTREE |
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| 40 | argtype:tree |
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| 41 | arglabel:Input tree |
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| 42 | argchoice: |
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| 43 | |
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| 44 | arg:PROTOCOL |
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| 45 | arglabel:Protocol |
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| 46 | argtype:choice_menu |
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| 47 | argchoice:Thorough tree search:thorough |
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| 48 | argchoice:Quick tree search:quick |
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| 49 | argchoice:Add to tree:add |
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| 50 | argchoice:Optimize tree:optimize |
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| 51 | argchoice:Calculate branchlengths:calcblen |
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| 52 | argchoice:Calculate bootstraps:bootstrap |
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| 53 | argchoice:Score tree:score |
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| 54 | |
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| 55 | arg:MODEL |
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| 56 | argtype:chooser |
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| 57 | arglabel:Model |
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| 58 | argchoice:GTRGAMMA (standard, max 10k seqs):GTRGAMMA |
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| 59 | argchoice:GTRCAT (faster, min 150 seqs):GTRCAT |
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| 60 | |
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| 61 | arg:REPEATS |
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| 62 | argtype:choice_menu |
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| 63 | arglabel:Searches\n(Thorough+Optimize only) |
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| 64 | argchoice:1:1 |
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| 65 | argchoice:5:5 |
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| 66 | argchoice:10:10 |
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| 67 | argchoice:20:20 |
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| 68 | argchoice:50:50 |
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| 69 | argchoice:100:100 |
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| 70 | |
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| 71 | arg:BOOTSTRAPS |
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| 72 | argtype:choice_menu |
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| 73 | arglabel:Bootstraps |
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| 74 | argchoice:No:no |
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| 75 | argchoice:Auto:autoMRE_IGN |
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| 76 | argchoice:5:5 |
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| 77 | argchoice:10:10 |
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| 78 | argchoice:20:20 |
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| 79 | argchoice:50:50 |
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| 80 | argchoice:100:100 |
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| 81 | argchoice:200:200 |
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| 82 | argchoice:500:500 |
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| 83 | argchoice:1000:1000 |
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| 84 | |
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| 85 | arg:MRETREE |
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| 86 | argtype:choice_menu |
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| 87 | arglabel:Compute MRE consensus tree\n(only with bootstraps) |
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| 88 | argchoice:No:-nomre |
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| 89 | argchoice:Yes: |
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| 90 | |
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| 91 | arg:TREENAME |
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| 92 | argtype:text |
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| 93 | arglabel:Tree name |
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| 94 | argtext:raxml |
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| 95 | |
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| 96 | arg:SEED |
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| 97 | argtype:text |
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| 98 | arglabel:Random seed\n(empty=use time) |
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| 99 | argtext: |
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| 100 | |
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| 101 | arg:THREADS |
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| 102 | argtype:text |
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| 103 | arglabel:CPU thread override\n(empty=autodetect) |
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| 104 | argtext: |
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(=calculate likelihood and append to comment)
