RAW README From Sean Eddy

SQUID - library of functions for biological sequence analysis Copyright (C) 1992-2002 Washington University School of Medicine

SQUID is a freely redistributable library of C code functions for sequence analysis. SQUID also includes a number of small utility programs.

To install squid, see the file: INSTALL -- instructions for installing the programs

If you have any questions about redistributing squid or using squid code in your own work, see the files: COPYRIGHT -- copyright notice, and information on my distribution policy LICENSE -- version 2 of the GNU Public License (see COPYRIGHT)

For a web page with more information on squid, see: http://www.genetics.wustl.edu/eddy/software/#squid

You can always download the latest stable release of squid from: ftp://ftp.genetics.wustl.edu/pub/eddy/software/squid.tar.gz

The development codebase is available by anonymous CVS: cvs -d :pserver:anonymous@skynet.wustl.edu:/repository/sre login (password "anonymous") cvs -d :pserver:anonymous@skynet.wustl.edu:/repository/sre checkout squid

If you encounter any bugs in this library, or you have any questions or comments, please e-mail me at the address below. Due to limited personal time, I may not respond, but I do read all my mail.

Sean Eddy eddy@genetics.wustl.edu

HHMI/Dept. of Genetics Washington University School of Medicine 660 South Euclid Box 8232 Saint Louis Missouri 63110 USA

Changes with this program

I only keep the program named sreformat, which can convert various file formats like fasta, a2m(aligned fasta) and so on.

Help information in sreformat

  Output format choices: Unaligned      Aligned
                         -----------    -------
                         fasta          stockholm
                         embl           msf
                         genbank        a2m
                         gcg            phylip
                         gcgdata        clustal
                         pir            selex
                         raw            eps

  Available options are:
    -h : help; print brief help on version and usage
    -d : force DNA alphabet for nucleic acid sequence
    -r : force RNA alphabet for nucleic acid sequence
    -l : force lower case
    -u : force upper case
    -x : convert non-IUPAC chars in DNA to N's for IUPAC/BLAST compatibility

Install this program

Please follow these commands:

make -j16
make install prefix=/path/to/you/wish

Then the program will generate two files: /path/to/you/wish/bin/sreformat and /path/to/you/wish/man/man1/sreformat.1.

If you want to see manual file, you can use this command:

man /path/to/you/wish/man/man1/sreformat.1