DIPLOMO, PC programme for phylogenetic dist. anal. from ANU

reisner at angis.su.oz.au reisner at angis.su.oz.au
Mon Nov 8 22:41:25 EST 1993


--------------------------------------------------------------
           DIPLOMO: A new approach to phylogeny
--------------------------------------------------------------

 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 life.anu.edu.au


We are pleased to annouce version 1.02 of 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
Site name:      life.anu.edu.au
Directory:      /pub/molecular_biology/software/diplomo
File name:      dipxxx.exe  (where xxx is the version number)
File type:      binary (self extraction archive)
- Alternatively you can obtain DIPLOMO using gopher
Name=DIPLOMO
Host=life.anu.edu.au
Port=70
Type=I
Path=1/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.

                             -=-=-=-=-=-=-

Questions and answers to DIPLOMO...
===================================


WHAT DOES DIPLOMO DO?
---------------------
 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?
--------------------------------
 - 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?
------------------------------------------------------------
 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?
----------------------------------
 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


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


 




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