Here are answers to a few frequently asked questions (FAQs) from new users of DNA Stacks package. Some of these answers are a bit complicated, so email me at the above address if you still have problems.
Please note that I am in the process of updating documentation for DNA Stacks, but some out of the provided on-line or file help is out-of-date.
Doug Eernisse 12/26/95
1. Where do I get current versions of the stacks package?
2. What do I do with the file 'dnastacks_xxx.sea.hqx'?
You need to debinhex the file. Binhex format is a standard way to transfer Mac files over computer lines and there are several programs that can debinhex it (e.g., Stuffit Expander (recommended), Binhex 4.0, Compact Pro, Stuffit). Most current transfer programs do the binhex conversion automatically (e.g., Fetch, TurboGopher, Netscape). Debinhexing will result in a file lacking the '.hqx' suffix that still needs to be decompressed before you can use it. This part is simple, provided that you have ample disk space. Click on the file and choose an appropriate destination location for the expanded folder and files.
3. Why am I having trouble decompressing the file 'dnastacks_xxx.sea'?
Make sure that you are not trying to expand it to your floppy drive, because there will not be enough disk space. Instead, expand it to your hard drive which should have at least a few MB disk space available.
4. What version of HyperCard do the stacks require?
You will need HyperCard 2.0 or later (2.3.x is current version), or the HyperCard Player (distributed with recently purchased Macintosh computers) or a current HyperCard "player" application (freeware available from the usual Macintosh software archives). I have gone to some lengths to keep compatibility with at least the official versions of HyperCard and HyperCard Player. Besides the HyperCard application, you must have at least the "Home" stack on your disk. Other stacks that come with HyperCard are not required and you can archive them to floppy if you need the disk space (The new versions of HyperCard also like to have "Color Tools" and "Audio Tools" around). If you have multiple versions of HyperCard on your hard disk there shouldn't be too many problems but it may require that you first open the most current HyperCard 2.X application directly and then "Open Stack" to get to DNA Translator or Aligner. You probably can toss the older HyperCard and related stacks as the newer HyperCard can open older stacks (e.g., 1.2.x).
5. I am trying to use the coloring features of Aligner stack but no Color menu appears?
You need to adjust HyperCard's memory partition to a value well above the default. Aligner needs a minimum of about 3000K devoted to HyperCard in order to behave normally. With the System 7.x Finder (or 6.0.x MultiFinder) active, select "About the Finder" from the Apple menu. This will show you how much total RAM is installed in your Mac and how much is consumed by the System. For example, if you only have 5 MB total RAM then you might have roughly 3200K (3.2 MB) RAM not used by the System. Then you might try setting the HyperCard memory partion value to about 3000K. If you have 8 MB or more total RAM, you may find that 5 MB for HyperCard will keep the stack from experiencing memory limitations, especially if you wish to use an expanded card size (e.g., 1200 x 640 pixels) in Aligner, and then attempt to color the data. Note that it is a trade-off how much memory that you set aside for HyperCard and how much memory you leave for other programs. Also note that RAM is relatively cheap and easy to install these days.
6. So how do I increase the memory partition for HyperCard?
First, make sure that HyperCard is not active. From the Finder, click on the HyperCard (or HyperCard Player) application ONCE (not twice) to hilite it. Then select "Get Info" from the File menu. This will display a dialog box which has a "Suggested size" default memory partition value (1,050K for HyperCard 2.3) and "Minimum Size" and "Preferred Size" values that you can adjust. You can edit either of these values by typing 'tab' until the appropriate value is hilited and then typing in a new value (e.g., 4000). Close the dialog box and you are ready to open the stacks.
7. I have aligned data in XXXXXX format; how do I import it to Aligner?
Choose "Import Options..." from Aligner's Data menu. You will be asked to specify its format and select the input file. Various options include EuGene, GCG Pileup, Clustal V, Treealign, Nexus (only a "standard" Nexus format is supported), Phylip, Phylip output file (which includes the optional data matrix display), and an "interleave" format. A variety of these and other formats can likewise be exported by choosing "Export Options..." from Aligner's
Data menu. Note that most of these conversions were formerly available from DNA Translator's utility cards. You can still get there by selecting "Utility Card" from the "View" menu of Aligner but I am in the process of replacing the need for the latter cards.
8. I have separate unaligned sequences in XXXXXX format; how do I import them to Aligner?
If the sequences are in GenBank, EMBL, PIR, or various other formats, you can combine them to a single file using the provided "File Combiner" stack. Alternatively, you might find it easiest to assemble the unconverted sequences into a single text file with your favorite word processor or text editor, in whatever order you wish the sequences to be in. Then follow the instructions for number 7 above. It is recommended that when you import data to Aligner, you should choose the option of also saving them to disk. These will be saved in the default "named string" format (same as PAUP's "simple text" format).
9. I am still having trouble getting my data into Aligner. What should I do?
Look at the file in a word processor and compare it to the sample data files provided in the folder "Aligner Sample Data". Try importing the sample data using "Import String Sequences" from the Data menu of Aligner. You can also experiment with "Import Options..." using many of the files provided in the "Sample Input/Output Data" folder. If you have the program PAUP handy and can use one of its import options, first "Execute" the imported data in PAUP and then "Export" as "Simple Text" format. This is the default format that Aligner expects, except that Aligner expects that any period ('.') in your aligment indicates a gap, and any dash ('-') indicates a match character to the first sequence, whereas PAUP is more flexible.
10. How can I make slides or output printed text from the color display?
HyperCard does not print/output colored text directly, but it is quite easy to use various screen snapshot facilities to output what you see onscreen as a standard PICT image file, which then can be opened in a variety of graphics programs or pasted into word processor documents. My favorite utility for generating screen snapshots is the shareware control panel device, Flashit (3.0.2). Relatively inexpensive (ca. $600) color laser printers do an excellent job of printing color output files. Flashit can also be used in conjunction with a program such as Microsoft PowerPoint to make effective seminar slides of your alignments. The coloring performed
by Aligner is better suited for these uses than it is for interactive alignment.
