README -- GJO editor Saturday, July 20, 1991 Gary J. Olsen FIRST: If you appreciate the software and/or data (that is, if you want the service to continue), please let us know at RDP@scotty.life.uiuc.edu SECOND: If there are problems or errors with the data, please let us know at the above address. THRID: If there are problems with the programs, please let me (Gary Olsen) know at gary@scotty.life.uiuc.edu There are three items in this directory: 1. README_GJO_editor: This "README" file. Get this file using FTP "text" mode. 2. GJO_editor.VMS: A VAX/VMS BACKUP save set containing the RDP sequence data some software (described in detail below). Get this file using FTP "binary" mode. 3. to_save.exe: A VAX/VMS executable file that corrects a problem with VAX/VMS BACKUP save sets that have been transferred by FTP. Get this file using FTP "binary" mode. GENERAL NOTE: The executable files were compiled and linked under VMS 5.3. They may not run under version 4.X of the operating system due to changes in the system libraries. Please send e-mail to gary@scotty.life.uiuc.edu if this a problem for you. VAX/VMS Program and Data Distribution BACKUP save set Contents of the BACKUP save set ============================================================================== Ribosomal Database Project Release 1 16S.SEQ;1 1800 15-JUN-1991 21:10 473 prokaryotic small subunit rRNA sequences--no eukaryotes or organelles) in sequence program format. Put this file in any convenient directory. ============================================================================== SEQUENCE program and related files SEQUENCE.COM;4 5 5-JUL-1990 12:50 SEQUENCE.EXE;30 536 17-JUN-1991 19:52 SEQCOMHLP.LIS;6 272 17-JUN-1991 12:33 SEQKEYHLP.LIS;2 35 17-JUN-1991 12:34 SEQNOTES.LIS;2 1 17-JUN-1991 19:53 SEQPRINT.COM;1 1 21-JUN-1988 16:52 These files should be put into a single directory. The directory should be given the logical name SEQIMAGE (include the device in the logical name definition), e.g., $ DEFINE/nolog SEQIMAGE DUB0:[USR1.OLSEN.PROGS.SEQUENCE] To make running the sequence program easy, add a line like the following to your LOGIN.COM file: $ SEQUENCE :== @ SEQIMAGE:SEQUENCE Then, typing the word SEQUENCE (or whatever you prefer to put to the left of the :==) will display the sequence files in your current directory and start the sequence program. If you include a file name on the command line, it will be interpreted as the input file. ============================================================================== TREE program and related files TREE.EXE;5 170 12-AUG-1990 05:54 TREE.NOT;1 2 8-JUL-1990 15:03 TREEHELP.LIS;25 30 18-JUN-1991 13:10 HETERO.EXE;1 15 17-JUN-1991 20:43 LOG_TO_845.EXE;1 17 30-SEP-1990 18:45 These files should be in a single directory (it can be the same as the sequence program directory, but need not be). The directory should be assigned the logical name TREEIMAGE. Include the device in the logical name definition, e.g., $ DEFINE/nolog TREEIMAGE DUB0:[USR1.OLSEN.PROGS.TREE] To run the tree program, add the following to your LOGIN.COM file: $ TREE :== $ TREEIMAGE:TREE Then, typing the word TREE (or whatever you prefer to put to the left of the :==) will then run the tree program. If you include a file name on the command line, it will be interpreted as the input file. HETERO.EXE implements a correction for site-to-site differences in nucleotide substitution rates (see Olsen, G. J. 1987. The earliest phylogenetic branchings: Comparing rRNA-based evolutionary trees inferred with various techniques. Cold Spring Harbor Symp. Quant. Biol. 52: 825-838). The program requests a distance matrix file (from the editor SIMILARITY/TREE command) for input. The command also works on the combined distance/topology files from the TREE program. LOG_TO_845.EXE reads the log file written by the tree program (those obnoxious files that accumulate when you leave the program with the EXIT command, rather than the QUIT command), and converts the printed tree into a "Newick 8:45" format [suitable, with minor modification, for PAUP, PHYLIP, Treedraw, TreeTool (what's that?), and probably other programs as well]. ============================================================================== SaveSet Block Size Fixer TO_SAVE.EXE;2 8 18-JUN-1991 16:05 Utility program for restoring the correct block size to BACKUP save sets that have been transferred using FTP. It can be kept anywhere. When you run the program, it will ask for an input file name and an output file name. [When a VAX/VMS backup file (called a save set) is moved by FTP (this must be done in "binary" mode), the "block size" is erroneously set to 512 bytes. Although all of the data are correct, the BACKUP program will not read the resulting file. This program will copy the save set into an new file with the correct block size.] ============================================================================== Formatted Documentation PROGDOCS_SIT.HQX;1 277 18-JUN-1991 16:37 A BinHex converted (i.e., text character), StuffIt archive of the program documentation files formatted in Microsoft Word 4.0 on the Macintosh. You don't need these, but for those people with a Macintosh and a Laserwriter, they make a nice printed copy of the information available via on-line help. There are three basic steps to making this data accessible. 1. Use FTP, Kermit, or your favorite file transfer utility to move this (as a TEXT file) to the Macintosh. 2. Use StuffIt (or BinHex) to Decode the BinHex format. 3. Use StuffIt (or UnStuffIt) to extract the three MS Word files from the archive. Your local Macintosh guru should be able to help you. ==============================================================================