--- a/GEMBASSY-1.0.3/doc/text/gbaseentropy.txt	Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,243 +0,0 @@
-                                  gbaseentropy
-Function
-
-   Calculates and graphs the sequence conservation using Shanon uncertainty
-
-Description
-
-   This function calculates and graphs the sequence conservation in regions
-   around the start/stop codons using Shanon uncertainty (entropy). Smaller
-   values resemble higher conservation where the minumum value is 0 and the
-   maximum value is 2. The entropy is typically the lowest around position 0
-   (start/stop codon position).
-
-   The entropy H at position i with distribution P(i) is calculated as follows:
-   H(P(i)) = -sum(P(i,j) * log(2,P(i,j)))
-    
-   G-language SOAP service is provided by the
-   Institute for Advanced Biosciences, Keio University.
-   The original web service is located at the following URL:
-
-   http://www.g-language.org/wiki/soap
-
-   WSDL(RPC/Encoded) file is located at:
-
-   http://soap.g-language.org/g-language.wsdl
-
-   Documentation on G-language Genome Analysis Environment methods are
-   provided at the Document Center
-
-   http://ws.g-language.org/gdoc/
-
-Usage
-
-Here is a sample session with gbaseentropy
-
-% gbaseentropy refseqn:NC_000913
-Calculates and graphs the sequence conservation using Shanon uncertainty
-(entropy)
-Program compseq output file (optional) [nc_000913.gbaseentropy]: 
-
-   Go to the input files for this example
-   Go to the output files for this example
-
-   Example 2
-
-% gbaseentropy refseqn:NC_000913 -plot -graph png
-Calculates and graphs the sequence conservation using Shanon uncertainty
-(entropy)
-Created gbaseentropy.1.png
-
-   Go to the input files for this example
-   Go to the output files for this example
-
-Command line arguments
-
-Calculates and graphs the sequence conservation using Shanon uncertainty
-(entropy)
-Version: EMBOSS:6.5.7.0 GEMBASSY:1.0.1
-
-   Standard (Mandatory) qualifiers (* if not always prompted):
-  [-sequence]          seqall     Nucleotide sequence(s) filename and optional
-                                  format, or reference (input USA)
-*  -graph              xygraph    [$EMBOSS_GRAPHICS value, or x11] Graph type
-                                  (ps, hpgl, hp7470, hp7580, meta, cps, x11,
-                                  tek, tekt, none, data, xterm, png, gif, svg)
-*  -outfile            outfile    [*.gbaseentropy] Program compseq output file
-                                  (optional)
-
-   Additional (Optional) qualifiers: (none)
-   Advanced (Unprompted) qualifiers:
-   -position           selection  [start] Either 'start' (around start codon)
-                                  or 'end' (around stop codon) to create the
-                                  PWM
-   -patlen             integer    [3] Length of oligomer to count (Any integer
-                                  value)
-   -upstream           integer    [30] Length upstream of specified position
-                                  to create PWM (Any integer value)
-   -downstream         integer    [30] Length downstream of specified position
-                                  to create PWM (Any integer value)
-   -[no]accid          boolean    [Y] Include to use sequence accession ID as
-                                  query
-   -plot               toggle     [N] Include to plot result
-
-   Associated qualifiers:
-
-   "-sequence" associated qualifiers
-   -sbegin1            integer    Start of each sequence to be used
-   -send1              integer    End of each sequence to be used
-   -sreverse1          boolean    Reverse (if DNA)
-   -sask1              boolean    Ask for begin/end/reverse
-   -snucleotide1       boolean    Sequence is nucleotide
-   -sprotein1          boolean    Sequence is protein
-   -slower1            boolean    Make lower case
-   -supper1            boolean    Make upper case
-   -scircular1         boolean    Sequence is circular
-   -sformat1           string     Input sequence format
-   -iquery1            string     Input query fields or ID list
-   -ioffset1           integer    Input start position offset
-   -sdbname1           string     Database name
-   -sid1               string     Entryname
-   -ufo1               string     UFO features
-   -fformat1           string     Features format
-   -fopenfile1         string     Features file name
-
-   "-graph" associated qualifiers
-   -gprompt            boolean    Graph prompting
-   -gdesc              string     Graph description
-   -gtitle             string     Graph title
-   -gsubtitle          string     Graph subtitle
-   -gxtitle            string     Graph x axis title
-   -gytitle            string     Graph y axis title
-   -goutfile           string     Output file for non interactive displays
-   -gdirectory         string     Output directory
-
-   "-outfile" associated qualifiers
-   -odirectory         string     Output directory
-
-   General qualifiers:
-   -auto               boolean    Turn off prompts
-   -stdout             boolean    Write first file to standard output
-   -filter             boolean    Read first file from standard input, write
-                                  first file to standard output
-   -options            boolean    Prompt for standard and additional values
-   -debug              boolean    Write debug output to program.dbg
-   -verbose            boolean    Report some/full command line options
-   -help               boolean    Report command line options and exit. More
-                                  information on associated and general
-                                  qualifiers can be found with -help -verbose
-   -warning            boolean    Report warnings
-   -error              boolean    Report errors
-   -fatal              boolean    Report fatal errors
-   -die                boolean    Report dying program messages
-   -version            boolean    Report version number and exit
-
-Input file format
-
-   The database definitions for following commands are available at
-   http://soap.g-language.org/kbws/embossrc
-
-   gbaseentropy reads one or more nucleotide sequences.
-
-Output file format
-
-   The output from gbaseentropy is to a plain text file or the EMBOSS
-   graphics device.
-
-   File: nc_000913.gbaseentropy
-
-Sequence: NC_000913
--30,1.98284
--29,1.97873
--28,1.97692
--27,1.97595
--26,1.97094
--25,1.96777
--24,1.96272
--23,1.96288
--22,1.95707
-
-   [Part of this file has been deleted for brevity]
-
-21,1.93528
-22,1.94470
-23,1.95204
-24,1.93139
-25,1.95640
-26,1.95711
-27,1.93785
-28,1.96060
-29,1.94316
-30,1.92581
-
-
-Data files
-
-   None.
-
-Notes
-
-   None.
-
-References
-
-   Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
-      Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
-      for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
-
-   Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
-      large-scale analysis of high-throughput omics data, J. Pest Sci.,
-      31, 7.
-
-   Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
-      Analysis Environment with REST and SOAP Web Service Interfaces,
-      Nucleic Acids Res., 38, W700-W705.
-
-Warnings
-
-   None.
-
-Diagnostic Error Messages
-
-   None.
-
-Exit status
-
-   It always exits with a status of 0.
-
-Known bugs
-
-   None.
-
-See also
-
-   gbaseinformationcontent Calculates and graphs the sequence conservation
-                           using information content
-   gbaserelativeentropy    Calculates and graphs the sequence conservation
-                           using Kullback-Leibler divergence (relative
-                           entropy)
-
-Author(s)
-
-   Hidetoshi Itaya (celery@g-language.org)
-   Institute for Advanced Biosciences, Keio University
-   252-0882 Japan
-
-   Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
-   Institute for Advanced Biosciences, Keio University
-   252-0882 Japan
-
-History
-
-   2012 - Written by Hidetoshi Itaya
-   2013 - Fixed by Hidetoshi Itaya
-
-Target users
-
-   This program is intended to be used by everyone and everything, from
-   naive users to embedded scripts.
-
-Comments
-
-   None.
-