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First commit of old repositories
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 # benner-gonnet matrix
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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2 # ppam := 350
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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3 # print (DayhoffM (NewLogPAM1, pam));
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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4 # DayMatrix(Peptide, pam=350, Simil: max=12.362, min=-3.511, max offdiag=4.155,
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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5 # del=-18.727-1.396*(k-1))
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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6 A R N D C Q E G H I L K M F P S T W Y V *
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7 1.0 -0.2 0.0 0.0 0.4 0.0 0.1 0.5 -0.4 -0.4 -0.7 -0.1 -0.4 -1.4 0.3 0.6 0.4 -2.4 -1.4 0.0 -3.5
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8 -0.2 2.8 0.4 0.2 -1.3 1.0 0.6 -0.4 0.6 -1.5 -1.4 1.8 -1.1 -2.0 -0.4 0.1 0.0 -1.2 -1.2 -1.2 -3.5
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9 0.0 0.4 2.0 1.5 -1.1 0.6 0.9 0.5 0.8 -1.8 -1.9 0.7 -1.4 -2.0 -0.3 0.6 0.4 -2.4 -1.0 -1.3 -3.5
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10 0.0 0.2 1.5 2.9 -1.9 0.8 1.9 0.4 0.5 -2.4 -2.5 0.6 -1.9 -3.0 -0.2 0.5 0.2 -3.5 -1.8 -1.8 -3.5
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11 0.4 -1.3 -1.1 -1.9 9.3 -1.4 -1.7 -1.2 -0.8 -0.5 -0.7 -1.6 -0.4 -0.3 -1.8 0.1 -0.2 -0.4 -0.1 0.2 -3.5
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12 0.0 1.0 0.6 0.8 -1.4 1.2 1.1 -0.4 0.7 -1.1 -1.1 1.0 -0.7 -1.6 0.0 0.2 0.1 -1.9 -1.1 -0.9 -3.5
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13 0.1 0.6 0.9 1.9 -1.7 1.1 2.0 -0.2 0.4 -1.7 -1.8 0.9 -1.3 -2.5 0.0 0.3 0.1 -2.9 -1.7 -1.2 -3.5
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15 -0.4 0.6 0.8 0.5 -0.8 0.7 0.4 -0.7 3.3 -1.3 -1.1 0.5 -0.8 0.1 -0.5 0.0 -0.1 -0.3 1.5 -1.1 -3.5
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20 -1.4 -2.0 -2.0 -3.0 -0.3 -1.6 -2.5 -3.5 0.1 1.1 1.8 -2.1 1.4 5.1 -2.5 -1.8 -1.3 3.5 4.2 0.5 -3.5
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21 0.3 -0.4 -0.3 -0.2 -1.8 0.0 0.0 -0.7 -0.5 -1.6 -1.5 -0.2 -1.4 -2.5 5.6 0.4 0.2 -3.4 -2.0 -1.1 -3.5
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