FYI Re: FINGERPRINTING AND PHYLOGENETIC TREE

Matthew Sachs msachs at ADMIN.OGI.EDU
Thu Oct 7 11:04:49 EST 1993


>Hi, everybody.
>
>I am working on plant fingerprinting and need the methods to deal with my
>results
>such as `phylogenetic analysis using parsimony (PAUP)' or `phylogeny inference
>package (PHYLIP)' OR  some other packages or even manual methods.
>
>Does anybody have some ideas about how to get these kind of things? Any advice
>is welcomed.
>
>Thank you very much for your time
>
>
>Sincerely,
>
>
>Jiahui
>
>From: ZHU at JII.AFRC.AC.UK


Dear Jiahui,

The following is a posting of a portion of a readme file for your information.


"

        CONTENTS OF rdp.life.uiuc.edu: pub/RDP          (August 1, 1993)

                   Ribosomal Database Project (RDP)
               University of Illinois, Urbana, IL  USA

This directory contains the following subdirectories and files:

   000README.ALL        file containing 00README files from all directories

   00Acknowledgements   a file attributing the source(s) of data in
                        this directory

   00README             this file

   00RELEASE_NOTES.3.0  file describing the changes in the RDP database
                        for release 3.0

   LSU_rRNA             aligned data files, lists of organisms, and
                        secondary structure files for the large subunit
                        of ribosomal RNA sequences

   SSU_rRNA             aligned data files, lists of organisms, and
                        secondary structure files for the small subunit
                        of ribosomal RNA sequences

   programs             programs for ribosomal sequence analysis and
                        display

Each directory contains a 00README file which describes the contents of
the directory. The file 000README.ALL contains all the individual
00README files.  Sequences are offered in GenBank format (with
alignment gaps), but can be converted to other formats by the programs
available in the programs/Convert_aln and programs/Readseq
directories.

The following information describes the RDP database and the guidelines
for using data downloaded from the FTP service.
------------------------------------------------------------------------

The Ribosomal Database Project (RDP) has been established to help
scientists and others utilize the large and rapidly growing collection
of ribosomal sequence data; at present the project is limited to
ribosomal RNA sequences.

The RDP offers or will offer:
    (1) alignments of the various classes of ribosomal RNA sequences,
    (2) software useful in manipulating the sequence data, and
    (3) various services to the user community.

The alignments are phylogenetically ordered (as far as possible), and
the user may select which sequences and which portions of the
sequences he/she wishes to have.  In addition some sequences are
offered in secondary structural representation.

The software includes several sequence editors/environments useful in
handling and analyzing the sequences, other programs for sequence and
phylogenetic tree display, and sequence analysis packages.

The services at present include phylogenetic analysis of sequences,
and probe checking, and will include probe design and sequence
alignment and assessment in the future.

The above are available via ftp (rdp.life.uiuc.edu) and/or electronic
mail:  server at rdp.life.uiuc.edu
------------------------------------------------------------------------
 
Labeling Data:
  All data that are obtained from the anonymous ftp server at the
  University of Illinois in Urbana, Illinois by FTP downloading and
  appear in any printed document, machine-readable document, retrieval
  system, or publication must be clearly labeled in the following way:
 
  "Data used in preparing this _________[figure, table, paper, etc.]
   were derived from the Ribosomal Database Project (RDP) on the
   anonymous ftp server at the University of Illinois in Urbana,
   Illinois updated on __________[month, e.g., February] ____________
   [date], ________[year]."

Literature Citation:
  Research assisted by any RDP service should cite:
    Larsen N, Olsen GJ, Maidak, BL, McCaughey MJ,
    Overbeek R, Macke TJ, Marsh TL, and Woese CR,
    The ribosomal database project. Nucleic Acids Research
    21 (Supplement): 3021-3023, 1993.

Disclaimer:
  The Ribosomal Database Project makes no warranty (express,
  implied, or statutory) regarding any data stored within it,
  including without limitation implied warranties of merchantability,
  fitness for use, or fitness for a particular purpose.

Funding:
  The RDP is largely funded by the National Science Foundation, 
  Division of Instrumentation and Resources. 

Questions or Comments:
  The electronic mail address for RDP correspondence is 
            rdp at phylo.life.uiuc.edu

RDP Staff:
  Niels Larsen, Tom Macke, Bonnie Maidak, Terry Marsh, Michael McCaughey,
  Gary Olsen, and Carl Woese. 

Other and previous contributions by:
  Robin Gutell, WenMin Kuan, Michael Maciukenas, Ross Overbeek, 
  and Mitchell Sogin."




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