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<phytime run.id="example" output.file="out" mcmc.chain.len="1E+7" mcmc.sample.every="100"
mcmc.print.every="50" mcmc.burnin="10000" mutmap="no" r.seed="1567773784">
<!-- Tree topology -->
<topology>
<instance id="T1" init.tree="bionj" optimise.tree="yes"/>
</topology>
<!-- Model of rate variation across lineages -->
<lineagerates model="lognormal"/>
<!-- Substitution model -->
<ratematrices id="RM1">
<instance id="M1" model="HKY85" optimise.tstv="yes" tstv="4.0"/>
</ratematrices>
<!-- Freerate model of variation of rates across sites -->
<siterates id="SR1">
<instance id="R3" init.value="0.5"/>
<instance id="R2" init.value="1.0"/>
<instance id="R1" init.value="2.0"/>
<weights id="D1" family="freerates" optimise.freerates="yes">
<instance appliesto="R3" value="0.33"/>
<instance appliesto="R2" value="0.33"/>
<instance appliesto="R1" value="0.33"/>
</weights>
</siterates>
<!-- Nucleotide frequencies -->
<equfreqs id="EF1">
<instance id="F1" optimise.freqs="no"/>
</equfreqs>
<!-- Vector of edge lengths -->
<branchlengths id="BL1" >
<instance id="L1" optimise.lens="no"/>
</branchlengths>
<!-- Model assembly -->
<partitionelem id="partition1" file.name="./seq.txt" data.type="nt" interleaved="no">
<mixtureelem list="T1,T1,T1"/>
<mixtureelem list="M1,M1,M1"/>
<mixtureelem list="F1,F1,F1"/>
<mixtureelem list="R1,R2,R3"/>
<mixtureelem list="L1,L1,L1"/>
</partitionelem>
<clade id="Gymno1">
<taxon value="Gymno_Araucaria"/>
<taxon value="Gymno_Ginkgo"/>
<taxon value="Gymno_Juniperus"/>
<taxon value="Gymno_Sciadopitys"/>
</clade>
<clade id="Gymno2">
<taxon value="Gymno_Araucaria"/>
<taxon value="Gymno_Juniperus"/>
<taxon value="Gymno_Sciadopitys"/>
</clade>
<calibration id="cal1">
<lower>40</lower>
<upper>60</upper>
<!-- <appliesto clade.id="Gymno2"/> -->
<appliesto clade.id="Gymno1" probability="0.8"/>
<appliesto clade.id="Gymno2" probability="0.2"/>
</calibration>
<calibration id="cal2">
<lower>50</lower>
<upper>200</upper>
<appliesto clade.id="Gymno1">
</appliesto>
</calibration>
</phytime>
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