--- a/Hammock/settings/settings.prop	Fri Oct 20 02:50:43 2017 -0400
+++ b/Hammock/settings/settings.prop	Wed Nov 01 05:54:28 2017 -0400
@@ -1,11 +1,11 @@
 #Lines starting with hash (#) are ignored
 #Tool commands. Define full paths if needed. By default (not specified) means locations relative to .jar file in Hammock/dist foltder
-#clustalOmegaCommand=
-#hmmbuildCommand=
-#hmmsearchCommand=
-#hhmakeCommand=
-#hhsearchCommand=
-#reformatCommand=
+clustalOmegaCommand=clustalo
+hmmbuildCommand=hmmbuild
+hmmsearchCommand=hmmsearch
+hhmakeCommand=hhmake
+hhsearchCommand=hhsearch
+reformatCommand=reformat.pl
 #Directory for all temporal files. Define full path if needed. Default (not specified): /tmp
 #tempDirectory=
 #Temporal files subdirectories. Define full paths if needed. Default (not specified): directories in tempDirectory/Hammock_temp/[time]/
@@ -17,9 +17,9 @@
 #hhsearchOutDirectory=
 #fastaDatabaseFile=
 #Tool parameters. Generally, it is not recommended to change this section.
-clustalOmegaParameters=
+clustalOmegaParameters=--wrap=999999
 hmmbuildParameters=--enone --fragthresh 1.0 --hand --wnone --amino --seed 42
-hmmsearchParameters=--nobias --F1 0.5 --F2 0.05 --F3 1e-2 --nonull2 --seed 42
+hmmsearchParameters=--nobias --F1 0.5 --F2 0.05 --F3 1e-2 --nonull2 --notextw -E 999999 --seed 42
 hmmalignParameters=--outformat selex --amino --seed 42
 hhmakeParameters=-M a2m -id 100 -diff inf -pcm 3 -nocontxt -v 0
 hhsearchParameters=-norealign -alt 1 -corr 0 -shift 0 -ssm 0 -tags -nocons -nopred -nodssp -sc 0 -v 0 -z 2 -Z 500000 -local -p 0.0 -vit -b 100.0 -E 100.0 -e 100.0 -z 100