DIPLOMO - Phylogenetic analysis of sequence data

[David G Green]

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           DIPLOMO: A new approach to phylogeny
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          We are pleased to annouce version 1.0 of DIPLOMO


          Questions and answers to DIPLOMO...
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          WHAT DOES DIPLOMO DO?
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           DIPLOMO compares different distance measures with each other
          by displaying them as a scatter plot. It then helps one
          instantly identify all individual comparisons within the plot.


          WHAT CAN I SEE IN DIPLOMO PLOTS?
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           - The trends that occur in different distance measures and
          hence in the mutational changes that gave rise to the
          individual taxa compared.
           - The grouping of taxa with similar characteristics.
           - How different distance measures correlate.


          WHAT CAN I LEARN FROM A DIPLOMO ANALYSIS?
          -----------------------------------------
           Depending on the distance measures used many different
          questions can be addressed with a DIPLOMO analysis, some
          typical examples are:
           - Whether different (groups of) taxa exhibit specific
          mutational constraints or preferences.
           - Whether a group of taxa that have particular
          characteristics when examined by one pair of distance measures
          also stand out when different distance measures are applied.
           As an example, DIPLOMO would readily tell one, whether
          sequences that show a relatively high proportion of synonymous
          mutations also show a relatively high proportion of
          transitional changes.
           - Whether a particular distance measure is appropriate for
          deriving a phylogenetic tree.
           - Whether the relative speed of the molecular clock within
          members of a phylum is constant and hence whether the
          evolutionary time span that can be assigned to one part of a
          tree can be extrapolated to other parts of that tree.
           - Whether trees derived from different data subsets or
          obtained using different algorithms vary.


          WHAT ARE THE PRINCIPAL STEPS INVOLVED IN A DIPLOMO ANALYSIS?
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           1. Generating distance matrices using different distance
          measures and combining them in a single DIP-file.
           2. Plotting two of the distance matrices against each other.
           3. Visually identifying comparisons with interesting
          characteristics in the plot, and labelling these comparisons
          with specific colours and/or symbols. DIPLOMO will then
          display the taxa involved together with some statistical
          analysis.
           4. Repeating steps 2 and 3 with different distance matrices
          while retaining all previously assigned labels.


          HOW DO I GET MY DATA INTO DIPLOMO?
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           DIPLOMO requires a main data file in DIP-format. This DIP-
          file contains the names of all taxa and all the distance
          matrices to be analysed.
           We are currently developing DisCalc, a computer program that
          produces a DIP- file by compiling distance matrices from
          sequence alignments and other sources. Although DisCalc will
          become available soon, virtually every program that produces
          distance matrices can be used to produce the input data for
          DIPLOMO. As the DIP-file format is very simple little editing
          will be required.
          Note: See Appendix C for the DIPLOMO file formats.


          WHAT COMPUTER DO I NEED?
          ------------------------
          DIPLOMO is designed for being ported to multiple platforms
          with a variety of different operating systems and system
          configurations. A version for Microsoft windows is in
          preparation. Versions for Windows NT, OSII, and UNIX with
          Motif will follow soon.
          Version 1.00 runs in text mode and various graphics modes
          under DOS only.

          Minimal system requirements:
          IBM compatible computer.
          480 K RAM
          Floppy disk.

          Desired system requirements:
          IBM compatible computer with Intel 80286 processor or better
          (optional math co-processor is used if installed)
          VGA graphics compatible video card
          600 K RAM
          Hard disk
          mouse


          WHERE DO I GET DIPLOMO?
          -----------------------
          For non commercial use, DIPLOMO can be obtained free of charge
          from the Australian National University.

               1)  Obtaining DIPLOMO on the network

          You can obtain DIPLOMO via Internet using anonymous FTP
          Host name:     life.anu.edu.au
          Directory:     /pub/molecular_biology/software/diplomo
          File name:     dip100.exe
          File type:     binary (self extraction archive)

                   Gopher:
          Name=DIPLOMO - Phylogenetic analysis
          Host=life.anu.edu.au
          Port=70
          Type=1
          Path=molecular_biology/software/diplomo


               2)  Obtaining DIPLOMO on floppy disk
          To obtain DIPLOMO on floppy disk, send an empty disk
          (formatted for DOS) and a self addressed return envelope to
          the author.


          HOW TO CONTACT THE AUTHOR
          -------------------------
          You can contact the author by mail, fax or electronic mail
          using the following address:

           Dr. Georg Weiller
           Research School of Biological Sciences
           Australian National University
           Canberra, ACT 0200
           AUSTRALIA

           tel.: (61) 249-5916
           fax.: (61) 249-4437
           e-mail:  weiller at rsbs0.anu.edu.au
               weiller at life.anu.edu.au