This is the README file for version 1.40 of PIMA, our Pattern-Induced Multiple-sequence Alignment program (see RF Smith and TF Smith, 1992, Protein Engng 5:35). Further documentation can be found in the doc subdirectory. In particular doc/RELEASE-NOTES contains release notes. You can obtain a (source code) copy of the software via ftp from gc.bcm.tmc.edu (128.249.26.6) in the directory pub/software/pima under the name pima-1.40.tar.gz, or check the README-binary file (in the same ftp directory, or in the etc subdirectory of the source) for information on already compiled binary distributions. This software should compile and run on most UNIX systems with an ANSI C compiler. The files are compressed using gzip and must be uncompressed using gunzip. If you do not have the gunzip utility it is available via ftp from prep.ai.mit.edu in the pub/gnu directory under the name gzip-.tar, where will be something like 1.2.4 (i.e. gzip-1.2.4.tar). To extract the software run the command: gunzip -c pima-1.40.tar.gz | tar xf - This will create the directory pima-1.40 and you can proceed to change to this directory and compile. To compile pima run: 1) ./configure 2) make 3) make check 4) make install If you have a difficulty with one of the steps, it would be best to stop at that point. Either try to resolve the difficulty or contact us (see below). In particular if step #3 fails then there is something wrong and do not proceed to install the programs (step #4). By default the previous steps will install the PIMA programs in /usr/local/bin, data files in /usr/local/lib/pima, and man pages in /usr/local/man/man1. If the directory where everything should be installed is not /usr/local, then replace step #1 above with something like: 1) ./configure --prefix=/opt/software/pima If you would like to use different C compiler flags, then replace step #1 above with something like: 2) CFLAGS=-O2 ./configure See the file INSTALL for further installation information. Please send email to brent@bcm.tmc.edu or rsmith@bcm.tmc.edu if you have any questions, comments, or suggestions.