modified: settings.conf

settings.conf

@@ -13,8 +13,7 @@ ORGANISM="10090"	# Taxid of the reference organism (e.g. "10090" for M. musculus
 LEVEL="32523"		# Level at which to search for orthologues; 2759 (Eukaryota); 33208 (Metazoa); 7742 (Vertebrata); 32523 (Tetrapoda); 40674 (Mammalia)
 
 ## WORKING AND DATABASE DIRS 
-TMP="/media/data0/RaftCoEv"	# Working folder
-#TMP="/media/data0/v0.51"
+TMP="/tmp/autocoevDemo"	# Working folder
 DTB="/var/tmp/DB10v1"	# Folder where databases are unpacked
 
 ## THREADS UTILIZATION
@@ -36,7 +35,7 @@ GBLOCKSOPT="-b5=h"	# Gblocks oprions, e.g. allowed gaps: "-b5=h" (half), "-b5=n"
 ## PhyML OPTIONS
 PHYMLGBLOCKS="vanilla"	# Use Gblocks filtered MSA or not ("gblocks", "vanilla")?
 PHYMLOPTIONS=""		# Any additional options to pass to PhyML (e.g. "-m Blosum62")
-PHYMLGUIDE="exguide"	# Use external guide tree for PhyML ("exguide", "noguide")?
+PHYMLGUIDE="noguide"	# Use external guide tree for PhyML ("exguide", "noguide")?
 TREESROOT="rooted"	# Root the generated trees by TreeBeST? ("rooted" or "noroot")
 
 ## EXTERNAL TREE OPTIONS
@@ -46,7 +45,7 @@ ETREEROOT="rooted"	# Root the external tree after trimming for each MSA? ("roote
 PAIRINGMANNER="all"	# Pairing manner ("all" or "defined")
 MINCOMMONSPCS="20"	# Minimum number of common species per protein pair
 GBLOCKS="vanilla"	# Use Gblocks filtered MSA or not ("gblocks", "vanilla")?
-TREESCAPS="auto"	# Tree to use with CAPS ("auto", "phyml", "external")
+TREESCAPS="phyml"	# Tree to use with CAPS ("auto", "phyml", "external")
 INCR="1000"		# Divide folders of protein pairs into groups of e.g. 1000
 
 ## CAPS RUN-TIME OPTIONS