WHAT IS ALE?
-----------

Ale is an alignment editor for genetic sequences.
- Ale supports nucleic and amino sequences.
- Ale provides a powerful vocabulary of alignment manipulation commands.
- Ale can read and write alignments in GenBank, EMBL, Fast-A, and
  Phylip formats, in addition to its own format, designed for speedy
  access to large alignments.
- Ale is Free software; this means that Ale is distributed with full
  source code, and you are guaranteed the right to modify and
  redistribute its sources.  You can support and extend Ale in-house,
  if you want.

Check out the `docs' subdirectory, which contains a printable manual
(in PostScript form), and a manual formatted for on-line browsing
within Ale or GNU Emacs.

Ale's home repository is

   http://svn.red-bean.com/ale/repos/trunk

Use Subversion (http://subversion.tigris.org) to check out a working
copy of Ale.  Subversion is similar to CVS; if you're familiar with
one, you should have no trouble using the other.


INSTALLATION:
------------

To install and run Ale, you'll need:
- an ANSI Standard C compiler,
- GNU Emacs 21.1 or later

To build and install ale, just type

	./configure
	make install

and see what happens.  If this doesn't go off without a hitch, that's
a bug in Ale's build process; please report it.  (If you're building
from a working copy, you'll need to run ./autogen.sh before
./configure.)

You can also uninstall later, by typing

        make uninstall


WHERE SHOULD WE INSTALL ALE?
---------------------------

You can specify where to install Ale with the --prefix option.  For
example, if you want to put Ale in MUMBLEFROTZ/bin, and its utility
programs and lisp files in MUMBLEFROTZ/lib, build Ale like this:

	./configure --prefix=MUMBLEFROTZ
	make install

The default value for --prefix is guessed by looking for where GNU
Emacs was installed.  For example, if Emacs lives in /usr/local/bin, the build process will assume --prefix=/usr/local.


WHAT COMPILER SHOULD I USE?
--------------------------

Parts of Ale are written in ANSI Standard C.  If you don't have an
ANSI C compiler installed on your system, you'll get copious error
messages from your C compiler when you try to compile Ale.

If you have the GNU C compiler installed on your system, the build
process will use it (GNU CC is ANSI-compliant).  Otherwise, it will
use the ordinary system C compiler.


INVOKING:
--------

Just type "ale SEQUENCE-FILE-1 SEQUENCE-FILE-2 ..."


WHAT IF THE CONFIGURE SCRIPT GUESSES WRONG?
------------------------------------------

If your system is arranged normally, the configure script should do
its job correctly, with no assistance.  If Ale does not compile
correctly on an ordinary system, that is a bug; please tell us about
it, so we can fix the problem for future releases.

However, if your compilers have unusual names, your libraries appear
in unusual directories, or your system is otherwise outside the
configure script's ken, it may need some guidance.  If it creates
Makefiles containing incorrect information, the suggestions here may
help.


If you need to tell Ale to use a specific compiler (e.g. acc, the ANSI
C Compiler on some Solaris systems), run configure like this:

	rm -f config.cache
	CC=acc ./configure

If you have libraries installed in strange places, you'll need to help
the configure script find them.  For example, if you have the GDBM
library and header file in a directory named mumblefrotz, run
configure like this:

	rm -f config.cache
	CPPFLAGS=-Imumblefrotz LDFLAGS=-Lmumblefrotz ./configure