• Why are the sequence names not properly listed in the sequence selection list?  If the sequence names are not listed properly, there is most probably a format error in the input file.  Check the input file format and try again.
 
• Why gives my computer a ‘Log domain error’ while computing the evolutionary distance?  For example, when the computer gives a log-domain error when computing evolutionary distance according to the Jukes and Cantor model, the fraction of differences between two sequences exceeds  0.75.  In this case, the distance can not be computed (see equation of Jukes and Cantor, above).  If f > 0.75, the program crashes and gives a LOG DOMAIN error. When this happens, check the alignment and/or use the more conserved parts (or sequences) of the alignment to construct a tree with.

• Why is it not possible to apply rate calibration to the file ‘test.seq’. Because the ‘test.seq’ file contains not enough sequences to accurately apply rate calibration.   Files should contain at least about 35 sequences of 1000 or more nucleotide positions.

• Is there no print preview option?  No, unfortunately not, but the page boundary gives you an idea whether the tree will fit on the page or not.

• The option for converting file formats does not work.  Try to copy the ‘readseq.exe’ file and the input file (containing your sequence data) to your working directories.

• Why is it not possible to start the drawing program (or another program of the TREECON package) and gives my computer the ‘cannot run multiple instances’ message.  This message can only occur  when running Windows 3.1 and means that already one of the TREECON programs is running.  Since TREECON is a 32-bit program running under a 16-bit operating system (Windows 3.1 or 3.11), only one 32-bit program can be active at the same time.  Make sure all the programs are closed and start anew.

• Why is it not possible to do bootstrap analysis on a part of the sequence alignment or on only the first and second codon positions.   If you would like to perform bootstrap analyses on only a part (or selection) of the sequence alignment, it is necessary to make a new alignment, which only contains the region or positions one wants to consider.  This can be done with the ‘Tools’ option in TREECON.  Once the new sequence file has been made, bootstrap analyses can be performed.
 
• Why does TREECON no longer reads trees previously saved in the TREECON format.  In some cases (some distributions), TREECON no longer correctly reads trees previously saved in the TREECON format.  However, in most cases this can be easily solved by adding two zeros (0  0) to the list of bootstrap nodes and values (under the heading [BOOTSTRAP] in the '*.trc' file).

KNOWN BUGS (but not yet solved….)

• Sometimes, numbers instead of titles appear in the menu of the TREECON drawing program.  Although quite annoying, this is not a major problem.  Just select the menu item (if you recall what it does) or restart the drawing program.
 
• Sometimes, a tree saved in the bracket format cannot be read.  If this is the case, open the tree in a word processor such as notepad, and make sure the tree description fits on one line, and is not divided over several lines.  If this does

not help, please remove dots, hyphens, underscores, and other 'strange' characters that appear in the sequence names.  Sometimes, these non-alphabetical characters pose problems.  Another possibility is to send me the 'bracket' tree via email, so I can test it myself.  I will also try to correct these problems in the future.
 
• .....

ABOUT THE AUTHOR

Yves Van de Peer was born in Turnhout, Belgium on April 26th, 1965.  In 1987 he got his diploma as a biologist at the University of Antwerp.  Since then he is working in the research group of Rupert De Wachter, whose main interest is the evolution and structure of ribosomal RNAs.  The author is generally interested in the reconstruction of biological evolution by means of macromolecules, and in particular in developing new methods to infer evolutionary trees based on sequence data.   At the moment, Yves Van de Peer has a Postdoc position at the Department of Biochemistry (University of Antwerp, Belgium).

The author can be reached at the
Department of Biochemistry
University of Antwerp (UIA)
Universiteitsplein 1
2610 Wilrijk (Antwerpen)
Belgium
phone.: +32.3.8202316 (work)
             +32.15.321208 (home)
fax: +32.3.8202248
email: yvdp@uia.ua.ac.be

 
Five recent papers of the author are:
 
• Van de Peer, Y., Van der Auwera, G., De Wachter, R. (1996) The evolution of stramenopiles and alveolates as derived by "substitution rate calibration" of small ribosomal subunit RNA. J. Mol. Evol. 42, 201-210.
 
• Van de Peer, Y., Rensing, S., Maier, U.-G., De Wachter, R. (1996) Substitution rate calibration of small ribosomal subunit RNA identifies chlorarachniophyte endosymbionts as remnants of green algae.  Proc. Natl. Acad. Sci. USA 93, 7732-7736.
 
• Van de Peer, Y., Chapelle, S., De Wachter, R. (1996) A quantitative map of nucleotide substitution rates in bacterial ribosomal subunit RNA.  Nucleic Acids Res. 24, 3381-3391.
 
• Van de Peer, Y., De Wachter, R. (1997) Construction of evolutionary distance trees with TREECON for Windows: accounting for variation in nucleotide substitution rate among sites.  Comput. Applic. Biosci. 13, 227-230.
 
• Van de Peer, Y., De Wachter, R  (1997) Evolutionary relationships among the eukaryotic crown taxa taking into account site to site rate variation in 18S rRNA.  J. Mol. Evol. 45, 619-630.