ASAP command line: Brief Install and How to Description



******Install
you can install in 4 steps by typing the 4 following commands in a terminal
1) cd <dir where asap.tgz is located>
2) tar -xvzf asap.tgz
3) cd asap
4) make 
5) make clean
You should have a working asap script in your asap directory.

******Run:
If you are in a hurry and want as soon as possible to see asap working, just type 

./asap <file_name> 


<file_name> must be one of these files: 
-fasta alignment
-phylip distance file
-MEGA distance file (see MEGA information below)

./asap -h
will give you this help
	-h    : this help
		-r #  : nbr of replicates for statistical tests (default is 10^4)
		-b #  : nbr of best results to be reported (default is 10)
		-m    : if present the distance Matrix is supposed to be MEGA CVS (other formats are guessed)
		-a    : output all files: all probabilities, tree and graph files (default only graph files and 10 best agglomerations)
		-d #  : distance (0: Kimura-2P, 1: Jukes-Cantor --default--, 2: Tamura-Nei 3:simple distance)
		-o #  : NOT WORKING YET existent directory where results files are written (default is same dir than alignment)
		-t #  : transition/transversion (for Kimura) default:2




******Results: 
ASAP will print on screen the number of best results you choosed with -b option or the 10 best if no value is specified
It will produce some other files as 2 graphics files 


******Information

This software is delivered with  BIONJ C source code very slightly modified to construct the newick tree.

You can get more information on BIONJ here:
BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data." 
Gascuel O. Molecular Biology and Evolution. 1997 14:685-695



-------------------MEGA information---------------
Two MEGA distance files are read: 

*********
CVS file (default MEGA 5)  formated as follows:
[name 1],,
[name 2],##,,
...
[name n],##,##,... ##,,

You must specify a -m option on command line with this type of file

**********
default MEGA 4, formated as below
#mega
!Format DataType=Distance DataFormat=LowerLeft NTaxa=100
!other informations
	line
	line...
	
;
[1] #name 1
[2] #name 2
...
[n] #name n

[1 2.... n]
[1] 
[2] ##
[3] ## ##
...
[n] ## ## .....##

This mega format is assumed  as soon as the "#mega" keyword is present on 1st line
Some variations are tolerated in this latter format, but if you get an error you should try to stick to one above.