| 1 | <phyml run.id="lg4x" output.file="lg4x.tests" branch.test="no"> |
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| 2 | |
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| 3 | <!-- Tree topology: start with BioNJ and then SPRs --> |
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| 4 | <topology> |
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| 5 | <instance id="T1" init.tree="bionj" optimise.tree="no"/> |
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| 6 | </topology> |
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| 7 | |
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| 8 | |
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| 9 | <!-- Four rate matrices, read from files --> |
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| 10 | <ratematrices id="RM1"> |
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| 11 | <instance id="M1" model="customaa" ratematrix.file="../examples/lg4x/X1.mat"/> |
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| 12 | <instance id="M2" model="customaa" ratematrix.file="../examples/lg4x/X2.mat"/> |
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| 13 | <instance id="M3" model="customaa" ratematrix.file="../examples/lg4x/X3.mat"/> |
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| 14 | <instance id="M4" model="customaa" ratematrix.file="../examples/lg4x/X4.mat"/> |
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| 15 | </ratematrices> |
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| 16 | |
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| 17 | <!-- Freerate model of variation of rates across sites --> |
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| 18 | <siterates id="SR1"> |
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| 19 | <instance id="R1" init.value="0.197063"/> |
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| 20 | <instance id="R2" init.value="0.750275"/> |
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| 21 | <instance id="R3" init.value="1.951569"/> |
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| 22 | <instance id="R4" init.value="5.161586"/> |
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| 23 | <weights id="D1" family="freerates" optimise.freerates="yes"> |
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| 24 | <instance appliesto="R1" value="0.422481"/> |
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| 25 | <instance appliesto="R2" value="0.336848"/> |
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| 26 | <instance appliesto="R3" value="0.180132"/> |
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| 27 | <instance appliesto="R4" value="0.060539"/> |
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| 28 | </weights> |
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| 29 | </siterates> |
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| 30 | |
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| 31 | <!-- Amino-acid equilibrium frequencies are given by the models --> |
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| 32 | <equfreqs id="EF1"> |
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| 33 | <instance id="F1" aa.freqs="model"/> |
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| 34 | <instance id="F2" aa.freqs="model"/> |
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| 35 | <instance id="F3" aa.freqs="model"/> |
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| 36 | <instance id="F4" aa.freqs="model"/> |
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| 37 | </equfreqs> |
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| 38 | |
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| 39 | |
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| 40 | <!-- One vector of branch lengths --> |
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| 41 | <branchlengths id="BL1" > |
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| 42 | <instance id="L1" optimise.lens="yes"/> |
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| 43 | </branchlengths> |
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| 44 | |
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| 45 | |
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| 46 | <!-- Mixture model assemblage --> |
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| 47 | <partitionelem id="partition1" file.name="../examples/proteic" data.type="aa" interleaved="yes"> |
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| 48 | <mixtureelem list="T1, T1, T1, T1"/> |
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| 49 | <mixtureelem list="M1, M2, M3, M4"/> |
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| 50 | <mixtureelem list="F1, F2, F3, F4"/> |
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| 51 | <mixtureelem list="R1, R2, R3, R4"/> |
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| 52 | <mixtureelem list="L1, L1, L1, L1"/> |
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| 53 | </partitionelem> |
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| 54 | |
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| 55 | |
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| 56 | </phyml> |
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| 57 | |
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| 58 | |
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