Bioinformatics Software

Contents: Preface. 1. Clustal V multiple sequence alignments. 2. ClustalW version 1.7. 3. RasMol. 4. Oligo. 4. Mol script. 5. Tree view. 6. Alscript. 7. Phylip. Bibliography. Index.

To do a complete multiple alignments you new to know the approximate relationships of the sequences to each other which ones are most similar to each other. This is done by calculating a crude phylogenetic tree which is called a dendrogram. This dendrogram is used as a guide to align bigger and bigger groups of sequence during the multiple alignment. The OLTGO software has been broadly accepted as the industry software standard for selecting and analyzing oligonucleotides for various molecular biology applications. The first commercial version of the software has been introduced in 1989. The graphic commands create graphical objects that are rendered according to the graphics state at the point in the input file where the command is given. The commands need different arguments usually an atom or residue selection and sometimes also some explicit values. TREEVIEW is a programme for displaying and printing phylogenies. It is free and can be obtained on the Internet from the world wide web. It is designed to read most NEXUS and PHYLIP format tree files. It also supports drag and drop opening of files. (jacket)