DCSE 3.0 alignment editor for X-Windows

Peter.DeRijk derijkp at reks.uia.ac.be
Wed May 4 11:46:26 EST 1994


The multiple sequence alignment editor DCSE has been converted to 
X-windows, and is available for Silicon Graphics (IRIX). It uses the the 
great embedable language Tcl/Tk (Thanks, Dr. Ousterhout) for its interface. 
This way it is not only very easy to use, but also easily adaptable and 
extendable. Several interesting new features have been added (see 
attached readme file for more details).

DCSE 3.0 is currently only available for SGI systems, but other systems will 
follow. We will be installing some PC's with Linux shortly, so this will 
most probably be the next. I also would like to do a port to Sun, but do 
not have acces to one at the moment.

You can get DCSE v3.0 for X-Windows 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-SGI-3_0.TAR_Z
ftp> quit
% mv TKDCSE-SGI-3_0.TAR_Z tkdcse=sgi-3.0.tar.Z
% zcat tkdcse=sgi-3.0.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.

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


I have attached the readme file for DCSE 3.0 to this message.

================ readme ===================

What is DCSE
------------

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 v3.0 is compatible with the older version 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.

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.

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.

I will do my best to reply as fast as I can to any problems, etc.
. However, the development of DCSE is not my only task, which is
why my response might not be always as fast as you would like.

System
------
This program has been tested on an Indigo with an R4000 and on one
with an R3000. It should work on other Silicon Graphics machines as
well.

Installing the package
----------------------
Uncompress and untar the distribution in a suitable directory. This will
produce a directory called tkdcse_home. Go into that directory, and start
the program install. Then follow directions.

zcat tkdcse-sgi-3.0.tar.Z | tar xf -
cd tkdcse_home
./install

The install program will give you more info on what to do to install DCSE.

The programs can be started by typing 'tkdcse' or 'tkconvers' in a shell
window.

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.

How to contact me
-----------------

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




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