tkDCSE alignment editor available for Linux

Peter.DeRijk derijkp at reks.uia.ac.be
Mon Jul 3 05:30:27 EST 1995


tkDCSE for Linux is finally available. Version 3.4 is mainly for the
Linux port, and is not available for the other platforms. Maybe it will
be when I get the time to make new distributions. You can get the
package via WWW and anonymous ftp. Read the appended readme file for
more details. For those who don't know Linux (is this possible?): it is
a great free Unix clone, including X-Windows, which runs on plain
PC's.

Regards,

Peter De Rijk

----
Peter De Rijk			derijkp at reks.uia.ac.be
<a href="http://indigo2.uia.ac.be/~peter/personal/peter.html">Peter</a>

To achieve the impossible, one must think the absurd.
to look where everyone else has looked, but to see what no one else has seen.

DCSE v3.4 for X-Windows
-----------------------

The homepage for DCSE is available 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 v3.4
-------------------
This release is mainly for the port to Linux. Dynamic loading is not
available on Linux DCSE. Its main executable has the necessary extensions
statically linked. This might change once ELF is commonly available on Linux
systems. The descriptions in the help pages can be somewhat inaccurate about
this (They are the same as those for SGI and Sun systems, which do support dynamic
loading. 

Some other changes are:
- plugins: external programs/extensions to DCSE can be installed/deinstalled
  by adding or removing a directory in the plugins subdir.
- Unpatched Tcl and Tk libraries are now used: The problem of getting
  one environment variable TCL_LIBROOT do everything is solved by calling
  tkstartup.tcl directly, and hacking the info command using tcl code (in
  tclstartup.tcl)
- Standard installation now does not give group write permissions (was a
  possible security hole)
- dnapro and prodna added to Convers: used to translate a DNA alignment into
  a protein alignment, and vice versa. The original DNA sequences are
  recovered from the reference file when using prodna.
- several bugfixes

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
The package is split in two parts, so that they fit on diskettes.
tkdcse-linux-3.4.tar.gz: contains everything to run DCSE 
tcltkman-linux.tar.gz: contains the manual pages for Tcl/Tk, these are not necessary,
                       but can be useful when programming in Tcl.


Installing the package
----------------------

Uncompress and untar the distribution in a suitable directory. This will
produce a directory called tkdcse_home. The man pages for Tcl/Tk are not
in this distribution (so it fits on a floppy when compressed). If you
want to include these (only needed for programming), you should also get 
the file tcltkman-linux.tar.gz, and uncompress it in the tkdcse_home 
directory before installing. 
Go into the directory tkdcse_home, and start the program install. 
Then follow directions.

tar xvvzf tkdcse-linux-3.4.tar.Z
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.

tkdcse for Linux notes
----------------------
Many of the key combinations used in dcse (Alt-arrows, Control-arrows, 
Alt-Control-arrows) are by default used by the pager in fvwm. You can remove 
these by commenting out the following lines in the
/usr/X11/lib/X11/fvwm/system.fvwmrc file (system wide) or in your personal
.fvwmrc file:
#Key Left       A       M       Scroll -10 +0
#Key Right      A       M       Scroll +10 +0  
#Key Up         A       M       Scroll +0   -10
#Key Down       A       M       Scroll +0   +10
# press shift arrow + control anywhere, and move the pointer by 1% of a page
#Key Left       A       SC      CursorMove -1 0 
#Key Right      A       SC      CursorMove +1 +0  
#Key Up         A       SC      CursorMove +0   -1
#Key Down       A       SC      CursorMove +0   +1
# press shift arrow + meta key, and move the pointer by 1/10 of a page
#Key Left       A       SM      CursorMove -10 +0
#Key Right      A       SM      CursorMove +10 +0  
#Key Up         A       SM      CursorMove +0   -10
#Key Down       A       SM      CursorMove +0   +10


Dynamic loading of modules is not yet supported by tkDCSE for Linux. There
is one executable containing Tcl/Tk, BLT, Itcl, expect, and my own
extensions extraL and desc. This executable is called desc. The help pages
might not always be correct about this.


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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