academic/muscle: Update script and added manual page.

Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>

1 files changed, 26 insertions, 4 deletions

diff --git a/academic/muscle/README b/academic/muscle/README
index 4db82130b553c..2a8b2c538da0a 100644
--- a/academic/muscle/README
+++ b/academic/muscle/README
@@ -3,7 +3,29 @@ nucleotide sequences. A range of options is provided that give you the
 choice of optimizing accuracy, speed, or some compromise between the 
 two.
 
-For details and citation:
-Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high 
-accuracy and high throughput. Nucleic Acids Res. 32(5):1792-1797. 
-doi:10.1093/nar/gkh340
+Fast, accurate and easy to use
+MUSCLE is one of the best-performing multiple alignment programs
+according to published benchmark tests, with accuracy and speed that
+are consistently better than CLUSTALW. MUSCLE can align hundreds of
+sequences in seconds. Most users learn everything they need to know
+about MUSCLE in a few minutes—only a handful of command-line options
+are needed to perform common alignment tasks.
+
+NOTE about the "-stable" option no longer being supported:
+The "-stable" option had a bug, which sometimes resulted in incorrect
+alignments to be produced. The author has created a python script to
+be used as a workaround. The SlackBuild includes it and its usage is:
+
+  python muscle-stable.py input.fasta aligned.fasta > stable.fasta
+
+Papers
+There are two papers. The first (NAR) introduced the algorithm, and is
+the primary citation if you use the program. The second (in BMC Bio-
+informatics) gives more technical details, including descriptions of
+non-default options.
+
+Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high
+accuracy and high throughput. Nucleic Acids Res. 32(5):1792-1797
+
+Edgar, R.C. (2004) MUSCLE: a multiple sequence alignment method with
+reduced time and space complexity BMC Bioinformatics, (5) 113