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| 1 | # Menu for RAxML 8 |
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| 2 | # |
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| 3 | # use cases: |
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| 4 | # - build small publication dna tree |
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| 5 | # - multiple ml searches, pick best |
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| 6 | # - run bootstraps |
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| 7 | # - import best ml tree + support values |
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| 8 | # - import consensus from bootstraps |
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| 9 | # - build quick&dirty dna tree (or large tree) |
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| 10 | # - fast bootstraps |
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| 11 | # - import consensus |
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| 12 | # - build AA tree |
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| 13 | # - extend dna tree |
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| 14 | # - get support SH-like support values for tree |
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| 15 | |
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| 16 | # Options: |
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| 17 | # |
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| 18 | # sequence type: DNA, AA |
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| 19 | # tree size: large small |
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| 20 | # search type: fast slow |
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| 21 | |
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| 22 | # sequence type: DNA |
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| 23 | # tree size: small |
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| 24 | |
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| 25 | menu:Phylogeny max. Likelyhood |
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| 26 | |
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| 27 | item:RAxML 8 (DNA) |
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| 28 | itemmethod: ${ARB_XCMD} arb_raxml8.sh -p $PROTOCOL -m $MODEL -s $SEED -b $BOOTSTRAPS -r $REPEATS -nt -t "$THREADS" -f INPUTFILE & |
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| 29 | itemhelp:raxml8.help |
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| 30 | seqtype:N |
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| 31 | |
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| 32 | in:INPUTFILE |
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| 33 | informat:genbank |
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| 34 | insave: |
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| 35 | |
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| 36 | arg:PROTOCOL |
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| 37 | arglabel:Protocol |
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| 38 | argtype:chooser |
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| 39 | argchoice:Thorough:thorough |
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| 40 | argchoice:Quick:quick |
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| 41 | |
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| 42 | arg:MODEL |
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| 43 | argtype:chooser |
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| 44 | arglabel:Model |
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| 45 | argchoice:GTRGAMMA (standard, max 10k seqs):GTRGAMMA |
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| 46 | argchoice:GTRCAT (faster, min 150 seqs):GTRCAT |
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| 47 | |
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| 48 | arg:REPEATS |
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| 49 | argtype:choice_menu |
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| 50 | arglabel:Searches |
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| 51 | argchoice:1:1 |
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| 52 | argchoice:5:5 |
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| 53 | argchoice:10:10 |
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| 54 | argchoice:20:20 |
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| 55 | argchoice:50:50 |
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| 56 | argchoice:100:100 |
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| 57 | |
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| 58 | arg:BOOTSTRAPS |
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| 59 | argtype:choice_menu |
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| 60 | arglabel:Bootstraps |
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| 61 | argchoice:Auto:autoMRE_IGN |
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| 62 | argchoice:10:10 |
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| 63 | argchoice:20:20 |
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| 64 | argchoice:50:50 |
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| 65 | argchoice:100:100 |
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| 66 | argchoice:200:200 |
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| 67 | argchoice:500:500 |
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| 68 | argchoice:1000:1000 |
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| 69 | |
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| 70 | arg:SEED |
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| 71 | argtype:text |
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| 72 | arglabel:Random Seed |
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| 73 | argtext:123456 |
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| 74 | |
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| 75 | arg:THREADS |
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| 76 | argtype:text |
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| 77 | arglabel:CPU-Thread override |
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| 78 | argtext: |
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