Description: use phyml package instead of version source distributed with ARB
Author: Elmar Pruesse <elmar@pruesse.net>
Origin: other
--- a/GDE/Makefile
+++ b/GDE/Makefile
@@ -5,7 +5,6 @@
 	AxML/AxML.dummy \
 
 ARCHS_COMMON_NO_DEPENDS = \
-	PHYML20130708/PHYML20130708.dummy \
 
 # --------------------------------------------------------------------------------
 # If a package is available as debian package it should go here
@@ -26,6 +25,7 @@
 	FASTTREE/FASTTREE.dummy \
 	MAFFT/MAFFT.dummy \
 	MUSCLE/MUSCLE.dummy \
+	PHYML20130708/PHYML20130708.dummy \
 	PROBCONS/PROBCONS.dummy \
 
 # --------------------------------------------------------------------------------
--- a/GDEHELP/MENUS/phyml_20130708.menu
+++ b/GDEHELP/MENUS/phyml_20130708.menu
@@ -4,7 +4,7 @@
 #define PHYML_CALL(seqtype) \
         (   GOTO_LOCAL_DIR;GEN_PHYLIP(infile) && \
             RUN_IN_WINDOW(if [ "$TREE" != "tree_?????" -a ! -z "$TREE" ]; then arb_export_tree $TREE > input_tree.in; INPUT_TREE_PARAM=-uinput_tree.in; fi; \
-                          ($ARBHOME/bin/phyml_20130708 \
+                          (phyml \
                           --input=infile \
                           --datatype=seqtype \
                           --model=$MODEL \
