JWS-112 Bumping version of ClustalW (src, binaries and windows) to version 2.1.

[jabaws.git] / binaries / src / clustalw / src / Help.cpp

diff --git a/binaries/src/clustalw/src/Help.cpp b/binaries/src/clustalw/src/Help.cpp
index a2e354d..8b1c390 100644 (file)
--- a/binaries/src/clustalw/src/Help.cpp
+++ b/binaries/src/clustalw/src/Help.cpp
@@ -319,7 +319,7 @@ Help::Help()
     
     s.marker = "5";
     s.title = "Help for output format options.";
-    s.content = "Six output formats are offered. You can choose any (or all 6 if you wish).  \n"
+    s.content = "Several output formats are offered. You can choose any (or all 6 if you wish).  \n"
 "\n"
 "CLUSTAL format output is a self explanatory alignment format.  It shows the\n"
 "sequences aligned in blocks.  It can be read in again at a later date to\n"
@@ -330,6 +330,9 @@ Help::Help()
 "alignments (e.g. PRETTY, PROFILEMAKE, PLOTALIGN).  It is the same as the GCG\n"
 ".msf format files (multiple sequence file); new in version 7 of GCG.\n"
 "\n"
+"Fasta output cis widely used because of it's simplicity. Each sequence name is\n"
+"preceeded by a '>'-sign. The sequence itself is printed out in the following lines\n"
+"\n"
 "PHYLIP format output can be used for input to the PHYLIP package of Joe \n"
 "Felsenstein.  This is an extremely widely used package for doing every \n"
 "imaginable form of phylogenetic analysis (MUCH more than the the modest intro-\n"
@@ -645,7 +648,7 @@ Help::Help()
 "-TYPE=       :PROTEIN or DNA sequences\n"
 "-NEGATIVE    :protein alignment with negative values in matrix\n"
 "-OUTFILE=    :sequence alignment file name\n"
-"-OUTPUT=     :GCG, GDE, PHYLIP, PIR or NEXUS\n"
+"-OUTPUT=     :CLUSTAL(default), GCG, GDE, PHYLIP, PIR, NEXUS and FASTA\n"
 "-OUTORDER=   :INPUT or ALIGNED\n"
 "-CASE        :LOWER or UPPER (for GDE output only)\n"
 "-SEQNOS=     :OFF or ON (for Clustal output only)\n"