Merge branch 'latest'

CMakeLists.txt

@@ -337,12 +337,11 @@ if (NOT IQTREE_FLAGS MATCHES "single")
         set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fopenmp -pthread")
     elseif (CLANG)
         set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -pthread")
-        if (APPLE)
+        if (APPLE OR WIN32)
             set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Xpreprocessor -fopenmp -pthread")
-            set (CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -Xpreprocessor -fopenmp -lomp")
+            set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -lomp")
         else()
             set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fopenmp -pthread")
-            set (CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -fopenmp")
         endif()
     endif()
 else()

main/phyloanalysis.cpp

@@ -4165,10 +4165,14 @@ void assignBootstrapSupport(const char *input_trees, int burnin, int max_count,
         const char *target_tree, bool rooted, const char *output_tree,
         const char *out_prefix, MExtTree &mytree, const char* tree_weight_file,
         Params *params) {
-    //bool rooted = false;
+    bool myrooted = rooted;
     // read the tree file
     cout << "Reading tree " << target_tree << " ..." << endl;
-    mytree.init(target_tree, rooted);
+    mytree.init(target_tree, myrooted);
+    if (mytree.rooted)
+        cout << "rooted tree detected" << endl;
+    else
+        cout << "unrooted tree detected" << endl;
     // reindex the taxa in the tree to aphabetical names
     NodeVector taxa;
     mytree.getTaxa(taxa);
@@ -4213,8 +4217,11 @@ void assignBootstrapSupport(const char *input_trees, int burnin, int max_count,
         }
         scale /= sg.maxWeight();
     } else {
-        boot_trees.init(input_trees, rooted, burnin, max_count,
-                tree_weight_file);
+        myrooted = rooted;
+        boot_trees.init(input_trees, myrooted, burnin, max_count,
+                        tree_weight_file);
+        if (mytree.rooted != boot_trees.isRooted())
+            outError("Target tree and tree set have different rooting");
         if (boot_trees.equal_taxon_set) {
             boot_trees.convertSplits(taxname, sg, hash_ss, SW_COUNT, -1, params->support_tag);
             scale /= boot_trees.sumTreeWeights();

tree/iqtree.cpp

@@ -3733,7 +3733,7 @@ void IQTree::writeUFBootTrees(Params &params) {
         NodeVector taxa;
         // change the taxa name from ID to real name
         trees[i]->getOrderedTaxa(taxa);
-        for (j = 0; j < taxa.size(); j++)
+        for (j = 0; j < taxa.size() - (int)rooted; j++)
             taxa[j]->name = aln->getSeqName(taxa[j]->id);
         if (removed_seqs.size() > 0) {
             // reinsert removed seqs into each tree

tree/mtree.cpp

@@ -692,7 +692,7 @@ void MTree::readTree(istream &in, bool &is_rooted)
             if (branch_len[0] == -1.0) branch_len[0] = 0.0;
             if (branch_len[0] < 0.0)
                 throw ERR_NEG_BRANCH;
-            is_rooted = true;
+            rooted = is_rooted = true;
             root = newNode(leafNum, ROOT_NAME);
             root->addNeighbor(node, branch_len);
             node->addNeighbor(root, branch_len);