--- theseus_align.orig	2020-03-03 21:42:45.000000000 -0500
+++ theseus_align	2020-03-03 21:44:29.000000000 -0500
@@ -44,14 +44,14 @@
 CAT="/bin/cat";
 SED="/usr/bin/sed";
 TEE="/usr/bin/tee";
-theseus="/usr/local/bin/theseus"; # where to find the THESEUS binary executable
+theseus="@@PREFIX@@/bin/theseus"; # where to find the THESEUS binary executable
 fastafile="theseus.fasta";
 filemapfile="theseus.filemap";
 alignmentfile="theseus.aln";
 
 # for MUSCLE -- http://www.drive5.com/muscle/
-alignprog="/usr/local/bin/muscle";
-align_cmd="${alignprog} -maxiters 32 -in ${fastafile} -out ${alignmentfile} -clwstrict";
+# alignprog="/usr/local/bin/muscle";
+# align_cmd="${alignprog} -maxiters 32 -in ${fastafile} -out ${alignmentfile} -clwstrict";
 
 # for PROBCONS -- http://probcons.stanford.edu/
 # alignprog="/usr/local/bin/probcons";
@@ -68,8 +68,8 @@
 #align_cmd="${alignprog} -outorder=input -infile=${fastafile} -outfile=${alignmentfile}";
 
 # for MAFFT -- http://www.biophys.kyoto-u.ac.jp/%7Ekatoh/programs/align/mafft/
-# alignprog="/usr/local/bin/mafft";
-# align_cmd="${alignprog} --maxiterate 1000 --localpair --clustalout ${fastafile} > ${alignmentfile}";
+alignprog="@@PREFIX@@/bin/mafft";
+align_cmd="${alignprog} --maxiterate 1000 --localpair --clustalout ${fastafile} > ${alignmentfile}";
 
 # for T_COFFEE -- http://igs-server.cnrs-mrs.fr/%7Ecnotred/Projects_home_page/t_coffee_home_page.html
 #alignprog="/usr/local/bin/t_coffee";