--- a/GEMBASSY-1.0.3/doc/text/ggcsi.txt	Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,204 +0,0 @@
-                                     ggcsi
-Function
-
-   GC Skew Index: an index for strand-specific mutational bias
-
-Description
-
-   ggcsi calculates the GC Skew Index (GCSI) of the given circular bacterial
-   genome. GCSI quantifies the degree of GC Skew. In other words, this index
-   represents the degree of strand-specific mutational bias in bacterial
-   genomes, caused by replicational selection. 
-   GCSI is calculated by the following formula:
-
-      GCSI = sqrt((SA/6000) * (dist/600))
-
-   where SA is the spectral amplitude of Fourier power spectrum at 1Hz,
-   and dist is the normalized Euclidean distance between the vertices of 
-   cumulative GC skew.
-
-   GCSI ranges from 0 (no observable skew) to 1 (strong skew), and Archaeal
-   genomes that have multiple replication origins and therefore have no
-   observable skew mostly have GCSI below 0.05. Escherichia coli genome has
-   values around 0.10.
-
-   Version 1 of GCSI required fixed number of windows (4096), but the new GCSI
-   version 2 (also known as generalized GCSI: gGCSI) is invariant of the number
-   of windows. GCSI version 1 is calculated as an arithmetic mean (as opposed
-   to the geometric mean of gGCSI) of SR (spectral ratio, the signal-to-noise
-   ratio of 1Hz power spectrum) and dist.
-   
-   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 ggcsi
-
-% ggcsi refseqn:NC_000913
-GC Skew Index: an index for strand-specific mutational bias
-Program compseq output file [nc_000913.ggcsi]: 
-
-   Go to the input files for this example
-   Go to the output files for this example
-
-Command line arguments
-
-   Standard (Mandatory) qualifiers:
-  [-sequence]          seqall     Nucleotide sequence(s) filename and optional
-                                  format, or reference (input USA)
-  [-outfile]           outfile    [*.ggcsi] Program compseq output file
-
-   Additional (Optional) qualifiers: (none)
-   Advanced (Unprompted) qualifiers:
-   -gcsi               selection  [2] GCSI version to use
-   -window             integer    [4096] Number of windows. Must be a power of
-                                  2 (Any integer value)
-   -purine             boolean    [N] Use purine skew for calculation
-   -keto               boolean    [N] Use keto skew for calculation
-   -at                 boolean    [N] Use AT skew for calculation
-   -pval               boolean    [N] Calculate p-value when GCSI version 2 is
-                                  selected
-   -[no]accid          boolean    [Y] Include to use sequence accession ID as
-                                  query
-
-   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
-
-   "-outfile" associated qualifiers
-   -odirectory2        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
-
-   ggcsi reads one or more nucleotide sequences.
-
-Output file format
-
-   The output from ggcsi is to a plain text file.
-
-   File: nc_000913.ggcsi
-
-Sequence: NC_000913 GCSI: 0.0966615833014818 SA: 487.218569030757 DIST: 69.037726
-
-
-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
-
-   gb1          Calculate strand bias of bacterial genome using B1 index
-   gb2          Calculate strand bias of bacterial genome using B2 index
-   gdeltagcskew Calculate strand bias of bacterial genome using delta GC skew
-                index
-   gldabias     Calculate strand bias of bacterial genome using linear
-                discriminant analysis (LDA)
-
-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.
-