SUMMARY: RnaViz has been developed to easily create nice, publication quality drawings of RNA secondary structure. RnaViz 2 supports CT, DCSE, and RNAML input formats and improves on many aspects of the first version, notably portability and structure annotation. RnaViz is written using a hybrid programming approach combining pieces written in C and in the scripting language Tcl/Tk, making the program very portable and extensible. AVAILABILITY: Source code, binaries for Linux and MS Windows, and additional documentation are available athttp://rrna.uia.ac.be/rnaviz/

MOTIVATION: To improve the estimation of evolutionary distances between nucleotide sequences by considering the differences in substitution rates among sites. RESULTS: TREECON for Windows (Van de Peer,Y. and De Wachter,R. Comput. Applic. Biosci., 9, 569-570, 1994) is a software package for the construction and drawing of phylogenetic trees based on distance data computed from nucleic acid and amino acid sequences. For nucleic acids, we here describe the implementation of a recently developed method for estimating evolutionary distances taking into account the substitution rate of individual sites in a sequence alignment. AVAILABILITY: TREECON for Windows is available on request from the authors. A small fee is asked in order to support the work and to reinvest in new computer hard- and software. More information about the program and substitution rate calibration can be found at URL http:/(/)bioc-www.uia.ac.be/u/ yvdp/treeconw.html.

Yves Van de Peer, Rupert De Wachter; TREECON for Windows: a software package for the construction and drawing of evolutionary trees for the Microsoft Windows en

A package of programs (run by a management program called TREECON) was developed for the construction and drawing of evolutionary trees. The program MATRIX calculates dissimilarity values and can perform boostrap analysis on nucleic acid sequences. TREE implements different evolutionary tree constructing methods based on distance matrices. Because some of these methods produce unrooted evolutionary trees, a program ROOT places a root on the tree. Finally, the program DRAW draws the evolutionary tree, changes its size or topology, and produces drawings suitable for publication. Whereas, MATRIX is suited only for nucleic acids, the modules TREE, ROOT and DRAW are applicable to any kind of dissimilarity matrix. The programs run on IBM-compatible microcomputers using the DOS operating system.

DCSE provides a user-friendly package for the creation and editing of sequence alignments. The program runs on different platforms, including microcomputers and workstations. Apart from available hardware, the program is not limited in the size of the alignment it can handle. It deviates more from classical text editors than other available sequence editors because it uses a different approach towards editing. It shifts characters or entire blocks of aligned characters, rather than inserting or deleting gaps in the sequences. Alignment of a new sequence to an existing alignment is partly automated. Although DCSE can be used on protein sequence alignments, it is especially targeted at the examination of RNA. The secondary structure for every sequence can be incorporated easily in the alignment. DCSE also has extensive built-in support for finding and checking secondary structure elements. A sophisticated system of markers allows notation of special positions in an alignment. This system can be used to store information such as the position of hidden breaks, introns and tertiary structure interactions.