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Download ForCon 1.0 - Online manual

Author: Jeroen Raes | Contact: Yves van de Peer

General Information

ForCon is a user-friendly software tool for the conversion of nucleic acid and amino acid sequence alignments. Many software packages for sequence alignment and the construction of evolutionary trees have implemented their own standard of saving and reading sequence alignments. To circumvent the labourious work of manually converting alignment formats with the use of a word processor, this program was written: it converts these formats automatically.

ForCon is able to convert in both ways, i.e. reading and writing the following formats

(or formats used by the following software packages):
  • EMBL
  • Hennig86
  • MEGA
  • PAUP/Nexus
  • Parsimony Jackknifer
Other software packages are omitted, because they are usually able to read one of these formats.
A format for the publication of alignments can also be generated ("pretty").
Sequential and interleaved formats are both implemented in ForCon.

A selection of sequences or sequence positions can be made.

ForCon is also included in the software package TREECON.

Version Info

This is the very first version, so all sorts of things can ( and will, probably ) go wrong.
If you encounter any bugs, do not hesitate to report them: (but please be gentle).

Jeroen Raes

If you have any problems ( regarding the ForCon program, of course ... I'm a biochemist, not a marriage consultant ), you can always mail me. Please check the on-line help first !

Known bugs :

  • GCG format bug ( checksum values) ... fixed( 1 oct 1998 )
  • Win 98 gives a error message* when the program is already finished : don't worry : it works fine, but I'll see what I can do ( maybe I'll blame it on Gates ). There is no problem on other operating systems.

* "This program has made an illegal operation and will be shut down"

System Requirements

IBM compatible PC with

  • Win95
  • Win NT 3.5
  • Win NT 4.0
  • Win 3.1

ForCon takes up about 1.5Mb of your hard disk space.

The speed of the program depends on your computer, available RAM and the size of your sequence file.

Cting ForCon for Windows

Please use the following citation:

Raes, J. and Van de Peer,Y. (1999) ForCon : a software tool for the conversion of sequence alignments. EMBnet.news 6(1). Distributed for free at: http://vulcan.rug.ac.be/~jerae/ForCon/index.html.

Reprints are highly appreciated !


Jeroen Raes
Research group of Bioinformatics
Department of Plant Genetics
University of Ghent
K.L. Ledeganckstraat 35
B-9000 GENT

VIB / UGent
Bioinformatics & Evolutionary Genomics
Technologiepark 927
B-9052 Gent
+32 (0) 9 33 13807 (phone)
+32 (0) 9 33 13809 (fax)

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