DNA Translator and Aligner HyperCard Stacks Utilities to Aid Phylogenetic Analysis of Molecules Version 1.0n January 1994 Getting Started ¥¥ Quick Start ¥ Self-extracting Compacted Version The stacks and supporting files are compacted into a single file for distribution. Extract by double-clicking on the provided file from the Finder. When a dialog box appears, select your hard drive as the save location. ¥ Extracted Version Simply double-click on either the DNA Translator or Aligner stack icons. ¥¥ System Requirements ¥ Any Macintosh computer ¥ System Software 6.0.5 or greater, including System 7 or more recent ¥ 5 megabytes of RAM ¥ HyperCard 2.0 or above for System 6 and HyperCard 2.1 or above for System 7 users. ¥ A hard disk with at least 2 megabytes of free space. ¥ Memory partition for HyperCard set to 2.5 megabytes or more for faster performance and large stack windows full of lengthy or colored sequences. ¥¥ Folder Contents ¥ " Getting Started" is this document. ¥ "DNA Translator" is a stack that contains three separate parts. Codon cards construct graphs of codon usage data. Gene mapping cards display mitochondrial, chloroplast, or user-supplied genome maps. Utility cards are workbench of conversion or analysis tools for multiple sequence data files. ¥ "Aligner" is a stack specialized for display and manual editing of aligned sequence data. ¥ "Aligner Tutorial" is a document available from within a window in Aligner as long as you leave it as a "text only" file at its current location. ¥ "Sample Input/Output" is a folder containing miscellaneous file format examples and explanations for a few of the more specialized utilities. Try importing some of the provided input files while exploring the stacks. ¥ "FAQs" explains frequently asked and answered questions, especially concerning obtaining the stacks, RAM requirements, and colorizing sequence data in Aligner. ¥ "DNAstacks info" is a more complete summary of each stack's functions. ¥ "Sequences" is a folder containing all mitochondrial DNA sequences mapped on supplied gene mapping cards of DNA Translator. Leave these files named as they are in their current location if you expect to extract gene sequences from the maps. ¥ Disk versions may contain the compacted self-extracting archive "cpDNAseqs.sea" which are 3 large chloropast DNA sequences mapped on one of the gene mapping cards of DNA Translator. If you need these you could also use DNA Translator to convert GenBank/EMBL format versions of the sequences to the appropriate string format. ¥¥ Hints Set the memory partition for HyperCard to 2.5 megabytes or more for faster performance. This is done by selecting "Get Info" from the File menu while HyperCard is highlighted from the Finder. HyperCard 2.0 is NOT compatible with System 7 and will crash your computer. HyperCard comes with many stacks but only the HyperCard application and the Home stack are essential for using DNA Translator or Aligner. ¥¥ Availability The stacks are free for any noncommercial use and may not be sold without permission from the author. They also contain custom external resources with similar copyright restrictions detailed in the script for each stack. ¥¥ Feedback Please send your comments and suggestions to: Dr. Douglas J. Eernisse Museum of Zoology University of Michigan Ann Arbor, MI 48109-1079 Internet: Doug_Ee@um.cc.umich.edu Bitnet: Doug_Ee@umichum ¥¥ Published Description of Version 1.0 Eernisse, D. J. 1992. DNA Translator and Aligner: HyperCard utilities to aid phylogenetic analysis of molecules. Comput. Appl. Biosc. (CABIOS) 8: 177-184. ¥¥For demonstration of some of the newer features, see: Eernisse, D. J., and A. G. Kluge. 1993. Taxonomic congruence versus total evidence, and amniote phylogeny inferred from fossils, molecules, and morphology. Mol. Biol. Evol. 10:1170-1195. ¥¥ Release Notes A version history file for changes since version 1.0 is provided in the Sample Input/Output folder. ¥¥Notable recent features Added preliminary features to calculate synonymous and nonsynonymous changes, using the method of Nei and Gojobori (see: Gojobori, T., E.N. Moriyama, and M. Kimura. 1990. Chapt. 33. Statistical methods for estimating sequence divergence. Meth. Enzymol. 183: 531-550). This is one of the options for manipulating string sequences from DNA Translator's Utility Card "Convert" menu ("Sequence Report"). Added "Extract Nodes" feature, which allows automatic calculation of "Support Index" (also called "Decay Index") or "SI" values with PAUP. See the new intructions for this in the Sample Data:Specialized Instructions folder. Added (8/93) a color editor to the Aligner stack so that colors used can be changed.