--- a/GEMBASSY-1.0.3/doc/text/gicdi.txt	Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,210 +0,0 @@
-                                     gicdi
-Function
-
-   Calculates the intrinsic codon deviation index (ICDI)
-
-Description
-
-   gicdi calculates the intrinsic codon deviation index (ICDI). ICDI is a
-   measure to estimate codon bias of genes from species in which optimal
-   codons are not known. It is known to show high correlation with other
-   indices such as CBI and ENC. A gene using only one codon for each amino
-   acid will have an ICDI of 1, and a gene using every codon equally for
-   each amino acid will have an ICDI of 0.
-    
-   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 gicdi
-
-% gicdi refseqn:NC_000913
-Calculates the intrinsic codon deviation index (ICDI)
-Codon usage output file [nc_000913.gicdi]: 
-
-   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    [*.gicdi] Codon usage output file
-
-   Additional (Optional) qualifiers: (none)
-   Advanced (Unprompted) qualifiers:
-   -translate          boolean    [N] Include when translating using standard
-                                  codon table
-   -delkey             string     [[^ACDEFGHIKLMNPQRSTVWYacgtU]] Regular
-                                  expression to delete key (Any string)
-   -[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
-
-   gicdi reads one or more nucleotide sequences.
-
-Output file format
-
-   The output from gicdi is to a plain text file.
-
-   File: nc_000913.gicdi
-
-Sequence: NC_000913
-icdi,gene
-0.8192,thrL
-0.1258,thrA
-0.1127,thrB
-0.1689,thrC
-0.3099,yaaX
-0.2030,yaaA
-0.1600,yaaJ
-0.3533,talB
-
-   [Part of this file has been deleted for brevity]
-
-0.2203,yjjX
-0.2719,ytjC
-0.1377,rob
-0.2647,creA
-0.1944,creB
-0.1733,creC
-0.1926,creD
-0.2728,arcA
-0.5171,yjjY
-0.2434,yjtD
-
-
-Data files
-
-   None.
-
-Notes
-
-   None.
-
-References
-
-   Comeron JM, Aguade M. (1998) An evaluation of measures of synonymous codon
-      usage bias, J Mol Evol, 47(3):268-74.
-
-   Freire-Picos MA et al. (1994) Codon usage in Kluyveromyces lactis and in
-      yeast cytochrome c-encoding genes, Gene, 139:43-49.
-
-   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
-
-   gcbi      Calculates the codon bias index (CBI)
-   gdeltaenc Calculate the codon usage bias related to translation optimization
-             (delta ENC)
-   gsvalue   Calculate the strength of selected codon usage bias (S)
-
-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.
-