--- a/GEMBASSY-1.0.3/doc/text/gfop.txt	Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,209 +0,0 @@
-                                      gfop
-Function
-
-   Calculate the frequency of optimal codons (Fop)
-
-Description
-
-   gfop calculates the frequency of optimal codons (Fop).Fop is an index to
-   show the optimization level of synonymous codon usage choice. It is
-   basically a ratio of optimal codons against all codons used. The value
-   of Fop ranges from 0 (no optimal codons are used) and 1 (only optimal
-   codons are used).
-    
-   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 gfop
-
-% gfop refseqn:NC_000913
-Calculate the frequency of optimal codons (Fop)
-Codon usage output file [nc_000913.gfop]: 
-
-   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    [*.gfop] Codon usage output file
-
-   Additional (Optional) qualifiers: (none)
-   Advanced (Unprompted) qualifiers:
-   -translate          boolean    [N] Include when translates using standard
-                                  codon table
-   -[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
-
-   gfop reads one or more nucleotide sequences.
-
-Output file format
-
-   The output from gfop is to a plain text file.
-
-   File: nc_000913.gfop
-
-Sequence: NC_000913
-Laa,Lc,fop,gene
-20,5,0.4000,thrL
-819,133,0.4361,thrA
-309,46,0.4783,thrB
-427,69,0.5217,thrC
-97,7,0.2857,yaaX
-257,56,0.4643,yaaA
-475,96,0.3958,yaaJ
-316,56,0.6964,talB
-
-   [Part of this file has been deleted for brevity]
-
-169,27,0.2593,yjjX
-214,23,0.5652,ytjC
-288,49,0.4082,rob
-156,23,0.3478,creA
-228,26,0.3462,creB
-473,69,0.3478,creC
-449,70,0.3286,creD
-237,46,0.6957,arcA
-45,10,0.7000,yjjY
-227,24,0.2500,yjtD
-
-
-Data files
-
-   None.
-
-Notes
-
-   None.
-
-References
-
-   Ikemura, T. (1981) Correlation between the abundance of Escherichia coli
-      transfer RNAs and the occurrence of the respective codons in its protein
-      genes: a proposal for a synonymous codon choice that is optimal for the
-      E. coli translational system, J.Mol.Biol, 151:389-409.
-
-   Ikemura (1985) Codon usage and tRNA content in unicellular and multicellular
-      organisms, Mol.Biol.Evol, 2(1):13-34.
-
-   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
-
-   genc    Calculate the effective number of codons (Nc)
-   gew     Calculate a measure of synonymous codon usage evenness (Ew)
-   gscs    Calculates the scaled chi-square
-   gwvalue Calculate the 'relative adaptiveness of each codon' (W)
-
-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.
-