diff --git a/partfinder/analysis_method.py b/partfinder/analysis_method.py
index 0f997fcd..3fcc8677 100644
--- a/partfinder/analysis_method.py
+++ b/partfinder/analysis_method.py
@@ -762,14 +762,25 @@ def setup(self):
         if the_config.min_subset_size == False:
             the_config.min_subset_size = 100
 
-        partnum = len(the_config.user_subsets)
-        the_config.progress.begin(1, 1)
+
+        # we start by putting all the partitions together.
+        # we do this because I don't like the idea of starting with user-defined
+        # partitions and trying to split them one by one. But I don't know if 
+        # this is really defensible. Still, we have to start somewhere.
+        # but doing it this way allows us to first estimate an ML tree with 
+        # all subsets separate, which is generally useful.
+        user_partnum = len(the_config.user_subsets)
 
         # Start with the most partitioned scheme
-        start_description = range(partnum)
+        start_description = [0]*user_partnum
         start_scheme = scheme.create_scheme(
             the_config, "start_scheme", start_description)
 
+        partnum = 1
+        the_config.progress.begin(1, 1)
+
+        print start_scheme.subsets
+
         if len(start_scheme.subsets)>1:
             log.error("The k-means algorithm is designed to analyse \
                 the entire alignment at once. To use it, please define a \
diff --git a/partfinder/raxml.py b/partfinder/raxml.py
index 9f7ef8e6..4f964e4a 100644
--- a/partfinder/raxml.py
+++ b/partfinder/raxml.py
@@ -71,6 +71,11 @@ def run_raxml(command):
 
 def run_raxml_pthreads(command, cpus):
     global _raxml_pthreads_binary
+
+    # fall back on standard raxml if the number of cpus is 1
+    if(cpus==1):
+        run_raxml(commmand)
+
     if _raxml_pthreads_binary is None:
         _raxml_pthreads_binary = util.find_program(_binary_name_pthreads)
     command = " ".join([command, "-T", str(cpus), " "])
@@ -115,6 +120,7 @@ def make_ml_topology(alignment_path, datatype, cmdline_extras, scheme, cpus):
     command = ''.join([command, " -w '%s'" % os.path.abspath(aln_dir)])
 
     run_raxml_pthreads(command, cpus)
+
     alndir, aln = os.path.split(alignment_path)
 
     fast_tree_path = os.path.join(alndir, "RAxML_fastTree.fastTREE")