Release 20180621

configure.ac

@@ -1,7 +1,7 @@
 #                                               -*- Autoconf -*-
 # Process this file with autoconf to produce a configure script.
 
-AC_INIT([PhyML],esyscmd([sh -c "echo "3.3." | tr -d '\n' ; echo "20180214" | tr -d '\n'"]),[[email protected]])
+AC_INIT([PhyML],esyscmd([sh -c "echo "3.3." | tr -d '\n' ; echo "20180621" | tr -d '\n'"]),[[email protected]])
 AM_INIT_AUTOMAKE([foreign])
 
 AC_CONFIG_SRCDIR([src/simu.c],[doc/phyml-manual.tex])

examples/phytime/dating_example.xml

@@ -1,12 +1,13 @@
-<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">
+<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">
 
   <!-- Tree topology -->
   <topology> 
     <instance id="T1" init.tree="bionj" optimise.tree="yes"/>
   </topology>
 
 
+  <!-- Model of rate variation across lineages -->
   <lineagerates model="lognormal"/>
 
   <!-- Substitution model -->
@@ -47,26 +48,30 @@
     <mixtureelem list="L1, L1, L1"/>
   </partitionelem>
 
-
-  <clade id="CLADE1">
-    <taxon value="Gymno_Cycas"/>
+  <clade id="Gymno1">
+    <taxon value="Gymno_Araucaria"/>
     <taxon value="Gymno_Ginkgo"/>
     <taxon value="Gymno_Juniperus"/>
+    <taxon value="Gymno_Sciadopitys"/>
   </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 id="Gymno2">
+    <taxon value="Gymno_Araucaria"/>
+    <taxon value="Gymno_Juniperus"/>
+    <taxon value="Gymno_Sciadopitys"/>
   </clade>
-  <calibration id="CAL2">
-    <lower>0</lower>
-    <upper>10000</upper>
-    <appliesto clade.id="CLADE2">
+
+  <calibration id="cal1">
+    <lower>40</lower>
+    <upper>60</upper>
+    <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>
 

src/free.c

@@ -414,6 +414,20 @@ void Free_Tree_Lk(t_tree *mixt_tree)
       for(i=0;i<3;i++) Free(tree->log_lks_aLRT[i]);
       Free(tree->log_lks_aLRT);
 
+      Free(tree->div_post_pred_extra_0);
+      Free(tree->sum_scale_cat_extra_0);
+      Free(tree->sum_scale_extra_0);
+      Free(tree->patt_id_extra_0);
+      Free(tree->p_lk_extra_0);
+      Free(tree->p_lk_tip_extra_0);
+
+      Free(tree->div_post_pred_extra_1);
+      Free(tree->sum_scale_cat_extra_1);
+      Free(tree->sum_scale_extra_1);
+      Free(tree->patt_id_extra_1);
+      Free(tree->p_lk_extra_1);
+      Free(tree->p_lk_tip_extra_1);
+
       Free(tree->unscaled_site_lk_cat);
 
       For(i,2*tree->n_otu-1) Free_NNI(tree->a_edges[i]->nni);
@@ -523,6 +537,7 @@ void Free_Edge_Lk(t_edge *b)
 {
   Free(b->tPij_rr);
   Free(b->Pij_rr);
+
   Free_Edge_Lk_Left(b);
   Free_Edge_Lk_Rght(b);
 }

src/main.c

@@ -318,6 +318,7 @@ int main(int argc, char **argv)
 #ifdef BEAGLE
                   finalize_beagle_instance(tree);
 #endif
+                  Free_One_Spr(tree->best_spr);
                   Free_Spr_List_One_Edge(tree);
                   Free_Spr_List_All_Edge(tree);
                   Free_Triplet(tree->triplet_struct);

src/make.c

@@ -421,8 +421,6 @@ void Make_Extra_Edge_Lk(t_tree *tree)
 
   tree->patt_id_extra_0  = (int *)mCalloc(tree->data->crunch_len,sizeof(int));
 
-
-
   tree->div_post_pred_extra_1 = (short int *)mCalloc(ns,sizeof(short int));
 
   tree->sum_scale_cat_extra_1 = (int *)mCalloc(MAX(tree->mod->ras->n_catg,tree->mod->n_mixt_classes),sizeof(int));

src/times.c

@@ -1686,7 +1686,6 @@ void TIMES_Randomize_Tree_With_Time_Constraints(t_cal *cal_list, t_tree *mixt_tr
   int i,j,nd_num,*cal_ordering,n_cal,swap,list_size,tmp,orig_is_mixt_tree,repeat,n_max_repeats,tip_num,*no_cal_tip_num,n_no_cal_tip_num,*permut;
   t_cal *cal;
   t_clad *clade;
-  int idx;
 
   assert(mixt_tree->rates);
 
@@ -1699,7 +1698,6 @@ void TIMES_Randomize_Tree_With_Time_Constraints(t_cal *cal_list, t_tree *mixt_tr
   n_max_repeats           = 1000;
   cal                     = NULL;
   clade                   = NULL;
-  idx                     = -1;
 
   // List node indices that are not in any calibration set
   no_cal_tip_num = NULL;

src/utilities.c

@@ -8220,6 +8220,8 @@ char *Bootstrap_From_String(char *s_tree, calign *cdata, t_mod *mod, option *io)
   s_tree = Write_Tree(tree,NO);
 
   Free_Spr_List_One_Edge(tree);
+  Free_One_Spr(tree->best_spr);
+  Free_Spr_List_All_Edge(tree);
   Free_Triplet(tree->triplet_struct);
   Free_Tree_Pars(tree);
   Free_Tree_Lk(tree);