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

[jabaws.git] / binaries / src / clustalw / clustalw_help

diff --git a/binaries/src/clustalw/clustalw_help b/binaries/src/clustalw/clustalw_help
index 25c5483..5c2c251 100644 (file)
--- a/binaries/src/clustalw/clustalw_help
+++ b/binaries/src/clustalw/clustalw_help
@@ -1,7 +1,7 @@
 
 
 
- CLUSTAL 2.0.12 Multiple Sequence Alignments
+ CLUSTAL 2.1 Multiple Sequence Alignments
 
 
 
@@ -44,7 +44,7 @@
  -STATS=file    :Log some alignents statistics to file
 
 
->> HELP 1 <<             General help for CLUSTAL W (2.0.12)
+>> HELP 1 <<             General help for CLUSTAL W (2.1)
 
 Clustal W is a general purpose multiple alignment program for DNA or proteins.
 
@@ -273,7 +273,7 @@ meaningful.
 
 >> HELP 5 <<             Help for output format options.
 
-Six output formats are offered. You can choose any (or all 6 if you wish).  
+Several output formats are offered. You can choose any (or all 6 if you wish).  
 
 CLUSTAL format output is a self explanatory alignment format.  It shows the
 sequences aligned in blocks.  It can be read in again at a later date to
@@ -284,6 +284,9 @@ GCG output can be used by any of the GCG programs that can work on multiple
 alignments (e.g. PRETTY, PROFILEMAKE, PLOTALIGN).  It is the same as the GCG
 .msf format files (multiple sequence file); new in version 7 of GCG.
 
+Fasta output cis widely used because of it's simplicity. Each sequence name is
+preceeded by a '>'-sign. The sequence itself is printed out in the following lines
+
 PHYLIP format output can be used for input to the PHYLIP package of Joe 
 Felsenstein.  This is an extremely widely used package for doing every 
 imaginable form of phylogenetic analysis (MUCH more than the the modest intro-
@@ -587,7 +590,7 @@ the minimum score over the whole matrix.
 -TYPE=       :PROTEIN or DNA sequences
 -NEGATIVE    :protein alignment with negative values in matrix
 -OUTFILE=    :sequence alignment file name
--OUTPUT=     :GCG, GDE, PHYLIP, PIR or NEXUS
+-OUTPUT=     :CLUSTAL(default), GCG, GDE, PHYLIP, PIR, NEXUS and FASTA
 -OUTORDER=   :INPUT or ALIGNED
 -CASE        :LOWER or UPPER (for GDE output only)
 -SEQNOS=     :OFF or ON (for Clustal output only)