diff --git a/src/cactus/refmap/cactus_graphmap.py b/src/cactus/refmap/cactus_graphmap.py
index 24ee6ca4d..74cf0f695 100644
--- a/src/cactus/refmap/cactus_graphmap.py
+++ b/src/cactus/refmap/cactus_graphmap.py
@@ -114,8 +114,7 @@ def graph_map(options):
             # load up the seqfile and figure out the outgroups and schedule
             config_wrapper.substituteAllPredefinedConstantsWithLiterals(options)
             mc_tree, input_seq_map, og_candidates = parse_seqfile(options.seqFile, config_wrapper, pangenome=True)
-            og_map = compute_outgroups(mc_tree, config_wrapper, set(og_candidates))
-            event_set = get_event_set(mc_tree, config_wrapper, og_map, mc_tree.getRootName())
+            event_set = get_event_set(mc_tree, config_wrapper, {}, mc_tree.getRootName())
 
             # apply path overrides.  this was necessary for wdl which doesn't take kindly to
             # text files of local paths (ie seqfile).  one way to fix would be to add support
diff --git a/src/cactus/refmap/cactus_refmap.py b/src/cactus/refmap/cactus_refmap.py
index f6f451bd3..35e2bd31f 100644
--- a/src/cactus/refmap/cactus_refmap.py
+++ b/src/cactus/refmap/cactus_refmap.py
@@ -297,8 +297,7 @@ def main():
         config_wrapper = ConfigWrapper(config_node)
         config_wrapper.substituteAllPredefinedConstantsWithLiterals(options)
         mc_tree, input_seq_map, og_candidates = parse_seqfile(options.seqFile, config_wrapper)
-        og_map = compute_outgroups(mc_tree, config_wrapper, set(og_candidates))
-        event_set = get_event_set(mc_tree, config_wrapper, og_map, mc_tree.getRootName())
+        event_set = get_event_set(mc_tree, config_wrapper, {}, mc_tree.getRootName())
 
         # apply path overrides.  this was necessary for wdl which doesn't take kindly to
         # text files of local paths (ie seqfile).  one way to fix would be to add support
diff --git a/src/cactus/setup/cactus_align.py b/src/cactus/setup/cactus_align.py
index 1b1e44143..b49d27444 100644
--- a/src/cactus/setup/cactus_align.py
+++ b/src/cactus/setup/cactus_align.py
@@ -260,7 +260,12 @@ def make_align_job(options, toil, config_wrapper=None, chrom_name=None):
     
     mc_tree, input_seq_map, og_candidates = parse_seqfile(options.seqFile, config_wrapper,
                                                           pangenome=options.pangenome)
-    og_map = compute_outgroups(mc_tree, config_wrapper, set(og_candidates), chrom_info_file = options.chromInfo)
+    if options.pangenome:
+        # outgroups not supported in pangenomes
+        # also, compute_outgroups() uses about 300 * N^2 bytes which can be huge for big pangenomes
+        og_map = {}
+    else:
+        og_map = compute_outgroups(mc_tree, config_wrapper, set(og_candidates), chrom_info_file = options.chromInfo)
     event_set = get_event_set(mc_tree, config_wrapper, og_map, options.root if options.root else mc_tree.getRootName())
     if options.includeRoot:
         if options.root not in input_seq_map: