FAMAP - a Fast Algorithm for constructing Multiple sequence
Alignment and Phylogeny

Release Date: 5 Jan 2014  



AVAILABILITY
------------
The package and related C source codes are available at
http://www.sta.cuhk.edu.hk/xfan/share/FAMAP.rar.



USAGE
-----
./FAMAP format infile LociSeq RootSeq



PARAMETERS
----------
format    a character giving the style of the input. This must 
          be one of "f" or "d". If "f", a file is input. If "d",
          a directory contains several files is input.
infile    name of the input file or directory.
LociSeq   name of the file contains the sequence for identification 
          of the sites. Only relevant if the user want to identify 
          the sites/sequence labels with a given sequence. 
RootSeq   name of the file contains the sequence for locating the root.
          Only relevant if the user want to locate the root by a given 
          sequence.



EXAMPLE
-------
./FAMAP f Tanaka.fas CRS.fasta african.fasta



OUTPUT
------
FAMAP_tree.txt       :  The output tree saved in Newick format.
FAMAP_dendrogram.txt :  The output dendrogram.
FAMAP_Alignment.txt  :  The aligned sequences in fasta format.
FAMAP_loci.txt       :  The alignment results with site id.



INSTALLATION
------------
If the source files are used, one can adopt the following command to compile.
g++ -o FAMAP test_treebuild.cpp



SEE ALSO
--------
For a complete description of the input/output formats of FAMAP, please
see the manual included in the package for Windows.



BUGS
----
If you encounter strange behaviour please contact:
mailto:easterlyng@gmail.com        
mailto:lichunstyle@hotmail.com        
mailto:xfan@sta.cuhk.edu.hk        
        
