Description: Adapt to new command-line arguments in MUSCLE 5
 The muscle package now ships version 5 of the program, which is a complete
 re-implementation and is not backwards-compatible.  This patch updates
 the command-line arguments passed to muscle.
Author: Charles Plessy <plessy@debian.org>

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Origin: vendor
Forwarded: no
Last-Update: 2022-12-15

--- seaview-5.0.5.orig/align.cxx
+++ seaview-5.0.5/align.cxx
@@ -1012,7 +1012,7 @@ void init_msa_algos(void)
   set_res_value("msa_name_1", "clustalo"); 
   set_res_value("msa_args_1", "-v -i %f.pir -o %f.out --outfmt=fasta");
   set_res_value("msa_name_2", "muscle"); 
-  set_res_value("msa_args_2", "-in %f.pir -out %f.out");
+  set_res_value("msa_args_2", "-align %f.pir -output %f.out");
   if (count < 2) {
     set_res_value("msa_algo_count", "2");
     set_res_value("alignment", "0"); /* clustal-omega is default starting msa method */
