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arMI: analytical residual Mutual Information 
--------------------------------------------
Computation of
- Mutual Information (MI)
- analytical residual Mutual Information (arMI)
- numerical residual Mututal Information (nrMI)
of all pairwise data vectors from a sequence alignment.
The program accepts FASTA alignments as input (--mali),
alternatively a random alignment (--random)
of specified depth (--nseq) and length (--lseq)
is created internally .

All sequences must be of the same length, gap symbols '.' can be included.
The default base set of 27 symbols is represented by ASCII values [64,90]
or synonymously symbols [@,Z], where '@' is the program-internal gap symbol.

The number of sequences must be in the range [2,1755],
deeper alignments will lead to an assertion exception.

Reference
---------
```
Jens Kleinjung, Anthony C.C. Coolen
A simple analytical formula to compute the residual Mutual Information between pairs of data vectors.
http://dx.doi.org/10.1101/041988
```

Install / Uninstall
-------------------
Please read the general 'INSTALL' instructions.
Otherwise use the following commands:
tar -zxvf arMI-1.1.0.tgz; cd arMI-1.1.0
./configure; make; make check; make install


Usage
-----
armi [--mali ... || --random ] [OPTIONS ...]
	INPUT SEQUENCE
	   --mali <input alignment>	(mode: optional, type: char  , default: void)
	   --nsubset <number of seqs.>	(mode: optional, type: int   , default: 0)
	RANDOM SEQUENCE
	   --random 			(mode: optional, type: no_arg, default: off)
	   --nseq <number of seqs.>	(mode: optional, type: int   , default: 8)
	   --lseq <length of seqs.>	(mode: optional, type: int   , default: 16)
	OUTPUT
	   --prefix <output prefix>	(mode: optional, type: char  , default: void)
	HELP
	   --cite			(mode: optional, type: no_arg, default: off)
	   --version			(mode: optional, type: no_arg, default: off)
	   --help


-------------------------------------------------------------------------------
Copyright (C) 2015 Jens Kleinjung
Copyright (C) 2015 Ton Coolen

Availability
------------
The program is made available under the GNU Public License for academic
scientific purposes, under the condition that proper acknowledgement
is made to the authors of the program in publications resulting from the use
of the program.

License
-------
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program.  If not, see <http://www.gnu.org/licenses/>.