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annotate phylogenies/place_fossil_ml.sh @ 0:5b9a38ec4a39 draft default tip

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author osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
date Tue, 11 Mar 2014 12:19:13 -0700
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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1 #!/bin/bash
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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2 datafile=$1 #binary datafile
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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3 model=BINGAMMA
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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4 morphmodel=MK
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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5 tree=$2
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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6 reps=100
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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7
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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8 raxmlHPC-PTHREADS-SSE3 -T 8 -f u -s $datafile -K $morphmodel -m $model -n galaxy -t $tree -N $reps
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
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9 raxmlHPC-PTHREADS-SSE3 -T 8 -f v -s $datafile -K $morphmodel -m $model -a RAxML_weights.galaxy -n fossil_weights -t $tree -N $reps