From 2b76ab52cbef7305666423f52d166f2dd75c70a8 Mon Sep 17 00:00:00 2001
From: guindon <stephane.guindon@gmail.com>
Date: Tue, 19 Jun 2018 15:11:50 +0200
Subject: [PATCH] Added example files for PhyTime

---
 examples/phytime/dating_example.xml | 75 +++++++++++++++++++++++++++++
 examples/phytime/seq.txt            |  0
 2 files changed, 75 insertions(+)
 create mode 100644 examples/phytime/dating_example.xml
 mode change 100755 => 100644 examples/phytime/seq.txt

diff --git a/examples/phytime/dating_example.xml b/examples/phytime/dating_example.xml
new file mode 100644
index 00000000..df8900c2
--- /dev/null
+++ b/examples/phytime/dating_example.xml
@@ -0,0 +1,75 @@
+<phytime run.id="June2018" output.file="out" mcmc.chain.len="1E+7" mcmc.sample.every="100"
+         mcmc.print.every="50" mcmc.burnin="10000" mutmap="no" r.seed="1">
+
+  <!-- Tree topology -->
+  <topology> 
+    <instance id="T1" init.tree="bionj" optimise.tree="yes"/>
+  </topology>
+  
+
+  <lineagerates model="lognormal"/>
+  
+  <!-- Substitution model -->
+  <ratematrices id="RM1">
+    <instance id="M1" model="HKY85" optimise.tstv="no" 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="no">
+      <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="CLADE1">
+    <taxon value="Gymno_Cycas"/>
+    <taxon value="Gymno_Ginkgo"/>
+    <taxon value="Gymno_Juniperus"/>
+  </clade>
+  <calibration id="CAL1">
+    <lower>290</lower>
+    <upper>452</upper>
+    <appliesto clade.id="CLADE1">
+    </appliesto>
+  </calibration>
+  <clade id="CLADE2">
+    <taxon value="Fagales_Juglans"/>
+    <taxon value="Ophioglossum"/>
+  </clade>
+  <calibration id="CAL2">
+    <lower>0</lower>
+    <upper>10000</upper>
+    <appliesto clade.id="CLADE2">
+    </appliesto>
+  </calibration>
+
+</phytime>
+
+
diff --git a/examples/phytime/seq.txt b/examples/phytime/seq.txt
old mode 100755
new mode 100644