diff --git a/test/paml/unrooted_present/association/run_altree b/test/paml/unrooted_present/association/run_altree
index 4fcc7dd0b9a24b362ca2ca5cf69eea3f28beab12..32437b8744baf1d4469ff12cf2dc0db51f2e19c6 100755
--- a/test/paml/unrooted_present/association/run_altree
+++ b/test/paml/unrooted_present/association/run_altree
@@ -2,11 +2,12 @@
 
 # To obtain the apomorphy list corresponding to the tree whose topology
 # has been reconstructed by phyML
-# paml uses the baseml.ctl file as the parameter file
-baseml
+# paml uses the baseml.ctl file as the parameter file baseml
 
 # To perform the association test
 # The outgroup must be sepcified for the association analysis (the tree 
 # must be rooted). The outgroup is kept for the association test)
-../../../../altree -i rst  -j nb_cas_control.txt  -a -t SNP \
---outgroup OUTG -p paml -r 1 -o 1_trio_ML.asso
+RA=../../../..
+env PERL5LIB=$RA/blib/lib:$RA/blib/arch:$RA \
+	$RA/progs/altree -i rst  -j nb_cas_control.txt  -a -t SNP \
+		--outgroup OUTG -p paml -r 10 -o 1_trio_ML.asso --data-qual qualitative