Multiple alignment editor for X-Windows tkDCSE 3.3 available

Peter.DeRijk derijkp at reks.uia.ac.be
Fri Nov 4 17:39:13 EST 1994


DCSE v3.3 for X-Windows
-----------------------

I have made a homepage for DCSE on our WWW server
http://www-rrna.uia.ac.be/~peter/dcse/index.html).
You can look there for more info. 

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.

What is new in v3.3
-------------------
Here are all (except those I forgot to write down) changes to the
previous version of DCSE. On of the main differences is the use of
shared objects and dynamic loading. This is the reason that this will
not run on Irix 4.0.5; You will need Irix 5.2.

INTERNALS
- extensions to Tcl are handled completely differently:
  - main executable is an adapted wish (tcl/tk) with dynamic loading 
    extension:
         - C-extensions can be dynamically loaded when needed by the 
           extinit command.
	 - desc is also a dynamcially loadable extension.
  - only the environment variable TCL_LIBROOT should be set. All 
    extension libraries and code are found in the directory 
    tkdcse_home/lib (to which TCL_LIBROOT should point).
- updated several extensions:
  - expect 5.9
  - Tix 3.6c
  - incr Tcl 1.5
  - tclX 7.3b
  - blt 1.7
- added some freebee extensions (I don't use them (yet))
  - Wigwam 1.5b
  - moreButtons 1.2
  - table 0.1
- made adding external functions a tiny bit easier
- extraL as a seperate extension library:
  adds list manipulation commands such as lfind, lsub, lcor, lload, 
  lfile, lmanip, lmath.
- added man/mann to help_path:
  You can now eg. type 'help button' in wish to get help on the button 
  widget (after you have typed a 'descinit').

PROGRAM
- added new alignment options:
  - Myers-Miller algorithm (uses much less memory).
  - added '1 to many' alignment
- made the intro screen smaller
- windows are the first time positioned by the user. A file is kept 
  (per user) which stores the last used positions for windows. The last 
  used position will be used the following times.
- selection of sequence lines to be loaded from file is faster.
  and the selection box shows the number of currently selected sequences.
- iconised windows show a nice bitmap
- added the possibility of using a cutoff value when copying o's
- added the noinsert option to the import function (also a change in syntax).
- added constraints to entries, numerical entries also got control buttons
- added load and save options to tkconvers sequence line selection box.

BUG FIXES
- output from protein alignments was not correct
- embref sometimes wrote wrong sequence after using arrow keys
- locked lines were not adapted after remove or create lines
- macros are now loaded at startup
- bug in save secondary fixed
- list of sequences in tkconvers
- forced recalculation of display after create consensus/empty line and 
  after (un)grouping


Getting the package
-------------------
You can get the package by anonymous ftp to www-rrna.uia.ac.be. It is 
under the directory pub/dcse. You can also get the distribution via WWW 
from the DCSE home page on the following URL 
http://www-rrna.uia.ac.be/~peter/dcse/index.html

Installing the package
----------------------
If you already have 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 don't care, you can do 'rm -r tkdcse_home' to just remove the older
version.)

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-3.3.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.

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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