DCSE 3.2 for X-Windows for Sun and SGI

Peter.DeRijk derijkp at reks.uia.ac.be
Sun Jul 31 17:31:43 EST 1994


DCSE v3.2 avaiable for Silicon Graphics and Sun.

The multiple sequence alignment editor DCSE for X-windows is now also
available for Sun (Solaris). Also some enhancements have been added
since the previous version.

Consider it as a beta though. I have quite extensively tested it, but I
can only use the Sun over a network, so there might be some quirks (hope not)
I will be on holliday for the next 2 weeks, so I won't be able to answer
email. If you have problems, you can mail me, and wait till I get back to
get an answer. Of course I'd rather have a mailbox filled with mails
saying everything worked right away than with bug reports when I come back. 

I have appended some notes on what tkDCSE does, and how to get it

Peter De Rijk
derijkp at reks.uia.ac.be

If you already have a version of tkdcse installed you should first
remove the old version.  It might be best though to keep it for a while
to see if everything works ok in the new version. You can do this by
going to the directory you put tkdcse_home in and doing:
mv tkdcse_home oldtkdcse_home
(if you can do 'rm -r tkdcse_home' to just remove the older version.)

You can get DCSE v3.2 for X-Windows on Sun (how to get the sgi version
obviously resembles this recipee; replace sun by sgi though) via
anonymous ftp on uiam3.uia.ac.be (143.169.8.1). To get it, 
do the following:
% ftp uiam3.uia.ac.be
login as anonymous
and give your email adress as a password.
ftp> cd [.dcse]
ftp> bin
ftp> get TKDCSE-SUN-3_2.TAR_Z
ftp> quit
% mv TKDCSE-SUN-3_2.TAR_Z tkdcse-sun-3.2.tar.Z
% zcat tkdcse-sun-3.2.tar.Z | tar xf -
% cd tkdcse_home
% ./install
Then read the help, and follow further instructions. If you have problems 
with it, please contact me. Of course, if you think it is good, or have 
writen nice extensions to it, you may also contact me.
Installation should be done in the directory where DCSE will reside

Peter De Rijk
derijkp at reks.uia.ac.be


I have attached parts of the HISTORY and README file for DCSE 3.2 to this message.

================ HISTORY ===================

DCSE v3.2
========= 
- Readseq and interface to it added to tkconvers
- Help system
  - removed help files from tclX: these were not used anyway
  - in interactive shell you can type things like 'help' or 'help tclcommands' to get 
    hypertext help window (after descinit)
- Handling of defaults
  - alternative color and font schemes for menus, buttons, etc can be
    loaded. Examples are present in the schemes directory. When saving a
    default file, the current scheme will be used further on in this
    directory.
  - when saving default file the current alignment font is written and it will be
    used instantly next time
  - for default colors tkdcse first looks in nuc.col, pro.col in current
    directory, then in home. This can be overridden in the default file
    (takes top of default values for color file)
- Fonts:
  - Selection of fonts has changed
  - redraw after fontchange has improved
- Main menu of tkconvers has improved
- Intro screen tkdcse has changed slightly
- tkconvers can be called from 'External' menu
- Bug fixes:
  - Fixes to the installation procedure: sets all permisions
  - basepairing: now gives error if one selection is to small instead
                 of crashing
  - doesn't add {} any longer to default values when doing add

DCSE v3.1
=========
The most important new thing is the port to Solaris.
Other enhancements are:
tkdcse
------
- added the lload command to desc: this returns the conents of a file in a list
- added the vertical search (you can eg. search for the complement of a column)
- DCSE asks to save your data before loading new sequences (and possibly losing changes).
- The second time you bring up the load sequences box will be a lot
  faster than it was (noticable on large datasets)
- added the setseq function: lets you set all selected characters to one
  character.
- some bug fixes
  - 'set line type' only worked on the first sequence line selected, now on all
    selected lines.
  - after loading a group, the screen is now redrawn
  - Position Mask is now updated after a global insert or delete
tkconvers
---------
- scanning of reference files: The tle option does not work when parts
  are not joined and no sort string is specified: tkconvers now checks
  for this combination, and gives an error on it.

================ README ===================

What is DCSE v3 (tkDCSE)
------------------------

DCSE (Dedicated Comparative Sequence Editor) is a multiple alignment
editor. It can be used to edit protein, DNA or RNA alignments. The
structure of the molecules can be incorporated in the alignment. It is
written in C, and it uses dynamic memory for most things. This means
you can almost edit any size of alignment with it. It offers lots of
features such as color display of characters and structure, automatic
alignment relative to sequences already aligned with others, sequence
grouping, sequence or pattern searching, marker system, checking of
incorporated RNA structure, on-line hypertext help, macros, and a lot
more.

This new version of DCSE has an easy to use, yet flexible and programmable
X-windows interface provided by the Tcl/Tk language. A complete on-line
hypertext help system is provided. 

Although DCSE v3 is compatible with version 2 of DCSE, its
implementation is completely different. The core of DCSE is implemented
as an object which can be controlled by giving commands to it from the
Tcl language, an easy to learn, yet flexible, interpreted language. The
interface is written as a Tcl program. This way the program can be
easily customized, and batch jobs are even possible.

This approach has several advantages:
 - the user can adapt the interface of DCSE completely to his own liking.
 - It is easy to create macros or programs wich extend DCSE.
 - external programs can also be controlled in Tcl, and seamlessly integerated.
 - Tcl/Tk exists for a great variety of computers, so porting should be 
   simplified.

Convers is a complementary program to DCSE which does things like
converting between different file-formats. The new version has been
written a set of commandline programs, which are controlled by a Tcl/Tk
interface.

Bugs
----
If you are having problems with the program contact me. I will
do my best to get it fixed. Please report any bugs you have
found. If possible, state your machine's hardware and software
configurations. Sending me a full description of the
circumstances in which the bug occurs, possibly with the data it
happened on, will help me tracking down a bug. If you have any
suggestions, you can also make them to me.

Citation
--------
A paper has been written about DCSE and this is submitted to and
accepted by CABIOS. If you have used the program to obtain
results in a paper you've written, please cite the following
reference:

Peter De Rijk and Rupert De Wachter
DCSE v2.54, an interactive tool for sequence alignment and
secondary structure research.
Comput. Applic. Biosci.

Reprints of articles in which DCSE is mentioned would be
welcomed.

How to contact me
-----------------
I will do my best to reply as fast as I can to any problems, etc.
. However, unfortunately the development of DCSE is not my only task,
which is why my response might not be always as fast as you would
like (although I get a very good average).

Peter De Rijk
University of Antwerp (UIA)
Department of Biochemistry
Universiteitsplein 1
B-2610 Antwerp

tel.: 32-03-820.23.16
fax: 32-03-820.22.48
E-mail: derijkp at reks.uia.ac.be

Legalities
----------
DCSE is Copyright Peter De Rijk, University of Antwerp (UIA), 1993

You may give this application to anyone, via any medium, so long
as it is delivered with ALL the supplied files and UNALTERED, and
it is not supplied on a disc you are charging for (except for
media and postage costs). I maintain copyright on all the
material supplied and reserve the right to amend these conditions
in cases where I deem misuse.

Disclaimer

This application is supplied free to everyone 'as is', I do not
give any guarantee that it is free of bugs, or supply any
warranty about its suitability for use. No liability will be
accepted for any damage to or loss of data as a result of using
this application. However, if there are any problems with it
and you notify me of them, I will probably do my best to rectify
them.




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