Help update

Author: agudys

README.md

@@ -54,6 +54,9 @@ cd FAMSA && make
 
 # export a pairwise identity (PID) matrix to the CSV format (square) 
 ./famsa -dist_export -pid -square_matrix ./test/adeno_fiber/adeno_fiber pid.csv
+
+# profile-profile alignment without refining output 
+./famsa -refine_mode off ./test/adeno_fiber/upgma.no_refine.part1.fasta ./test/adeno_fiber/upgma.no_refine.part2.fasta pp.fasta
 ```
 
 
@@ -120,6 +123,7 @@ Options:
 * `-keep-duplicates` - keep duplicated sequences during alignment (default: disabled - duplicates are removed prior and restored after the alignment)
 * `-gz` - enable gzipped output (default: disabled)
 * `-gz-lev <value>` - gzip compression level [0-9] (default: 7)
+* `-refine_mode <on | off | auto>` - refinement mode (default: `auto` - the refinement is enabled for sets <= 1000 seq.)
 
 
 ### Guide tree import and export

run.sh

@@ -20,3 +20,6 @@
 
 # export pairwise identity (PID) matrix to CSV format (square) 
 ./famsa -dist_export -pid -square_matrix ./test/adeno_fiber/adeno_fiber pid.csv
+
+# profile-profile alignment without refining output 
+./famsa -refine_mode off ./test/adeno_fiber/upgma.no_refine.part1.fasta ./test/adeno_fiber/upgma.no_refine.part2.fasta pp.fasta

src/core/params.cpp

@@ -89,12 +89,13 @@ void CParams::show_usage(bool expert)
 		<< "                     (default: disabled - duplicates are removed prior and restored after the alignment).\n\n"
 
 		<< "  -gz - enable gzipped output (default: " << bool2str[gzippd_output] << ")\n"
-		<< "  -gz-lev <value> - gzip compression level [0-9] (default: " << gzip_level << ")\n\n";
+		<< "  -gz-lev <value> - gzip compression level [0-9] (default: " << gzip_level << ")\n"
+		<< "  -refine_mode <on | off | auto> - refinement mode (default: auto - the refinement is enabled for sets <= " << thr_refinement << " seq.)\n\n";
+
 
 	if (expert) {
 		LOG_NORMAL << "Advanced options:\n"
 			<< "  -r <value> - no. of refinement iterations (default: " << n_refinements << ")\n"
-			<< "  -refine_mode <on|off|auto> - refinement mode (default: auto - the refinement is disabled for sets larger than " << thr_refinement << " seq.)\n"
 			<< "  -go <value> - gap open cost (default: " << gap_open << ")\n"
 			<< "  -ge <value> - gap extension cost (default: " << gap_ext << ")\n"
 			<< "  -tgo <value> - terminal gap open cost (default: " << gap_term_open << ")\n"