diff -Naur mafft-6.240/src/mafft-homologs.tmpl mafft-6.240.new/src/mafft-homologs.tmpl
--- mafft-6.240/src/mafft-homologs.tmpl	2006-10-01 20:31:38.000000000 -0400
+++ mafft-6.240.new/src/mafft-homologs.tmpl	2008-09-05 17:14:17.000000000 -0400
@@ -31,11 +31,22 @@
 #   -w        entire sequences are subjected to BLAST search 
 #             (default: well-aligned region only)
 
-
 require 'getopts'
+require 'tempfile'
+
+# create temporary files
+temp_vf = Tempfile.new("_vf").path
+temp_if = Tempfile.new("_if").path
+temp_pf = Tempfile.new("_pf").path
+temp_af = Tempfile.new("_af").path
+temp_qf = Tempfile.new("_qf").path
+temp_bf = Tempfile.new("_bf").path
+temp_rid = Tempfile.new("_rid").path
+temp_res = Tempfile.new("_res").path
 
-system( mafftpath + " --help > /tmp/_vf#{$$} 2>&1" )
-pfp = File.open( "/tmp/_vf#{$$}", 'r' )
+
+system( mafftpath + " --help > #{temp_vf} 2>&1" )
+pfp = File.open( "#{temp_vf}", 'r' )
 while pfp.gets
 	break if $_ =~ /MAFFT v/
 end
@@ -114,35 +125,38 @@
 	mafftopt += " " + $OPT_o + " "
 end
 
-system "cat " + ARGV.to_s + " > /tmp/_if#{$$}"
+system "cat " + ARGV.to_s + " > #{temp_if}"
 ar = mafftopt.split(" ")
 nar = ar.length
 for i in 0..(nar-1)
 	if ar[i] == "--seed" then
-		system "cat #{ar[i+1]} >> /tmp/_if#{$$}"
+		system "cat #{ar[i+1]} >> #{temp_if}"
 	end
 end
 
 nseq = 0
-ifp = File.open( "/tmp/_if#{$$}", 'r' )
+ifp = File.open( "#{temp_if}", 'r' )
 	while ifp.gets
 		nseq += 1 if $_ =~ /^>/
 	end
 ifp.close
 
-STDERR.puts "Performing preliminary alignment .. "
-if nseq == 1 then
-	system( "cp /tmp/_if#{$$}"  + " /tmp/_pf#{$$}" )
+if nseq >= 100 then
+	STDERR.puts "The number of input sequences must be <100."
+	exit
+elsif nseq == 1 then
+	system( "cp #{temp_if}"  + " #{temp_pf}" )
 else
+	STDERR.puts "Performing preliminary alignment .. "
 	if entiresearch == 1 then
-#		system( mafftpath + " --maxiterate 1000 --localpair /tmp/_if#{$$} > /tmp/_pf#{$$}" )
-		system( mafftpath + " --maxiterate 0 --retree 2 /tmp/_if#{$$} > /tmp/_pf#{$$}" )
+#		system( mafftpath + " --maxiterate 1000 --localpair #{temp_if} > #{temp_pf}" )
+		system( mafftpath + " --maxiterate 0 --retree 2 #{temp_if} > #{temp_pf}" )
 	else
-		system( mafftpath + " --maxiterate 1000 --localpair --core --coreext --corethr #{corethr.to_s} --corewin #{corewin.to_s} /tmp/_if#{$$} > /tmp/_pf#{$$}" )
+		system( mafftpath + " --maxiterate 1000 --localpair --core --coreext --corethr #{corethr.to_s} --corewin #{corewin.to_s} #{temp_if} > #{temp_pf}" )
 	end
 end
 
-pfp = File.open( "/tmp/_pf#{$$}", 'r' )
+pfp = File.open( "#{temp_pf}", 'r' )
 inname = []
 inseq = []
 slen = []
@@ -155,7 +169,7 @@
 end
 pfp.close
 
-pfp = File.open( "/tmp/_if#{$$}", 'r' )
+pfp = File.open( "#{temp_if}", 'r' )
 orname = []
 orseq = []
 nin = 0
@@ -188,7 +202,7 @@
 #p act
 
 
-afp = File.open( "/tmp/_af#{$$}", 'w' )
+afp = File.open( "#{temp_af}", 'w' )
 
 STDERR.puts "Searching .. \n"
 ids = []
@@ -209,10 +223,10 @@
 	end
 
 	if local == 0 then
-		command = "lynx -source 'http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?QUERY=" + inseq[i] + "&DATABASE=swissprot&HITLIST_SIZE=" + nadd.to_s + "&FILTER=L&EXPECT='" + eval.to_s + "'&FORMAT_TYPE=TEXT&PROGRAM=blastp&SERVICE=plain&NCBI_GI=on&PAGE=Proteins&CMD=Put' > /tmp/_rid#{$$}"
+		command = "lynx -source 'http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?QUERY=" + inseq[i] + "&DATABASE=swissprot&HITLIST_SIZE=" + nadd.to_s + "&FILTER=L&EXPECT='" + eval.to_s + "'&FORMAT_TYPE=TEXT&PROGRAM=blastp&SERVICE=plain&NCBI_GI=on&PAGE=Proteins&CMD=Put' > #{temp_rid}"
 		system command
 	
-		ridp = File.open( "/tmp/_rid#{$$}", 'r' )
+		ridp = File.open( "#{temp_rid}", 'r' )
 		while ridp.gets
 			break if $_ =~ / RID = (.*)/
 		end
@@ -224,9 +238,9 @@
 		while 1 
 			STDERR.printf "."
 			sleep 10
-			command = "lynx -source 'http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?RID=" + rid + "&DESCRIPTIONS=500&ALIGNMENTS=" + nadd.to_s + "&ALIGNMENT_TYPE=Pairwise&OVERVIEW=no&CMD=Get&FORMAT_TYPE=XML' > /tmp/_res#{$$}"
+			command = "lynx -source 'http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?RID=" + rid + "&DESCRIPTIONS=500&ALIGNMENTS=" + nadd.to_s + "&ALIGNMENT_TYPE=Pairwise&OVERVIEW=no&CMD=Get&FORMAT_TYPE=XML' > #{temp_res}"
 			system command
-			resp = File.open( "/tmp/_res#{$$}", 'r' )
+			resp = File.open( "#{temp_res}", 'r' )
 #			resp.gets
 #			if $_ =~ /WAITING/ then
 #				resp.close
@@ -247,17 +261,17 @@
 	else
 #		puts "Not supported"
 #		exit
-		qfp = File.open( "/tmp/_q#{$$}", 'w' )
+		qfp = File.open( "#{temp_qf}", 'w' )
 			qfp.puts "> "
 			qfp.puts inseq[i]
 		qfp.close
-		command = blastpath + "  -p blastp  -e #{eval} -b 1000 -m 7 -i /tmp/_q#{$$} -d #{localdb} > /tmp/_res#{$$}"
+		command = blastpath + "  -p blastp  -e #{eval} -b 1000 -m 7 -i #{temp_qf} -d #{localdb} > #{temp_res}"
 		system command
-		resp = File.open( "/tmp/_res#{$$}", 'r' )
+		resp = File.open( "#{temp_res}", 'r' )
 	end
 	STDERR.puts " Done.\n\n"
 
-	resp = File.open( "/tmp/_res#{$$}", 'r' )
+	resp = File.open( "#{temp_res}", 'r' )
 	while 1
 		while resp.gets
 			break if $_ =~ /<Hit_id>(.*)<\/Hit_id>/ || $_ =~ /(<Iteration_stat>)/
@@ -310,17 +324,15 @@
 afp.close
 
 STDERR.puts "Performing alignment .. "
-system( mafftpath + mafftopt + " /tmp/_af#{$$} > /tmp/_bf#{$$}" )
+system( mafftpath + mafftopt + " #{temp_af} > #{temp_bf}" )
 STDERR.puts "done."
 
-bfp = File.open( "/tmp/_bf#{$$}", 'r' )
+bfp = File.open( "#{temp_bf}", 'r' )
 outseq = []
 outnam = []
 readfasta( bfp, outnam, outseq )
 bfp.close
 
-
-
 outseq2 = []
 outnam2 = []
 
@@ -356,5 +368,3 @@
 	puts ">" + outnam2[i]
 	puts outseq2[i].gsub( /.{1,60}/, "\\0\n" )
 end
-
-system( "rm -rf /tmp/_if#{$$} /tmp/_vf#{$$} /tmp/_af#{$$} /tmp/_bf#{$$} /tmp/_pf#{$$} /tmp/_q#{$$} /tmp/_res#{$$} /tmp/_rid#{$$}" )
diff -Naur mafft-6.240/src/mafft.tmpl mafft-6.240.new/src/mafft.tmpl
--- mafft-6.240/src/mafft.tmpl	2007-04-03 19:16:51.000000000 -0400
+++ mafft-6.240.new/src/mafft.tmpl	2008-09-05 17:18:04.000000000 -0400
@@ -240,11 +240,14 @@
 		shift   
 	done;
 
-#	TMPFILE=/tmp/`basename $0`.`whoami`.$$.`date +%y%m%d%H%M%S`
-	TMPFILE=/tmp/$progname.$$
+        # create temporary directory; terminate script in case of failure
+	if ! TMPFILE=`mktemp -dt $progname.XXXXXXXXXX`; then
+          echo "Failed to create temporary directory"
+          exit 1
+        fi
+
 	umask 077
-	mkdir  $TMPFILE  || er=1
-	trap "rm -r $TMPFILE " 0
+	trap "rm -rf $TMPFILE " 0
 	if [ $# -eq 1 ]; then
 		if [ -r "$1" -o "$1" = - ]; then
 			cat "$1" | tr "\r" "\n" > $TMPFILE/infile