INSTALLATION

    Just extract all files from ACANA_<System>.tar.gz or ACANA_<System>.zip 
    to a directory by one of the following commands:

    	tar xvfz ACANA_<System>.tar.gz 
    OR
   	unzip ACANA_<System>.zip 

    Enter the directory ACANA_DIR, and follow the usage instructions below to run ACANA.
    
USEAGE

	Usage: ./ACANA -I inSeqFile
	
	----REQUIRED PARAMETERS WITH VALUE----
	
	-I Input sequence file in FASTA format
	
	----OPTIONAL PARAMETERS WITH VALUE----
	
	-S 	 The scoring matrix file name (default: dnaMatrix)
	-O 	 The output file name (default: $(inSeqFile).ACANA and $(inSeqFile).ACANA.loc
	             	 default:
	             	        global alignments: $(inSeqFile).ACANA
	             	        local alignments: $(inSeqFile).ACANA.loc
	             	        alignment scores: $(inSeqFile).ACANA.score
	-G 	 The opening gap penalty (default: -500)
	-A 	 The affine gap penalty (default: -25)
	-T 	 The factor for increasing minimum local alignment cutoff (default: 10)
	-C 	 The minimum length of local alignment (default: 100 for ACANA, 50 for ACANA_L)
	
	----OPTIONAL INDICATOR PARAMETERS----
	
	-L Only output non-overlapped local alignments
	-P The data are protein sequences. The default is DNA sequences
	-H Print the usage information
	-V Print the version information
	
INPUT SEQUENCE FORMAT

    The input sequence File must be in FASTA format. A sequence file can 
    contain multiple pairs of sequences, for example, if the file contains 
    following sequences:

    >specie1Seq1 
    aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa 
    >specie2Seq1 
    aaaaaaaaaaaaaaaaaaaaaaaaccccccccccccc

    >specie1Seq2 
    ccccccccccccccccccccccccccccccccccccc 
    >specie2Seq2 
    aaaaaaaaccccccccccccccccccccccccccccc

    >specie1Seq3 
    ttttttttttttttttttttttttttttttttttttt 
    >specie2Seq3 
    tttttttttttttttttttttttaaaaaaaaaaaaaa

    ACANA will align 3 pairs of sequences: specie1Seq1 and specie2Seq1, 
    specie1Seq2 and specie2Seq2, specie1Seq3 and specie2Seq3

OUTPUT

    By default, ACANA outputs three files with the following file extensions.

    1) *.ACANA: contains all pairwise global alignment in FASTA


    2) *.ACANA.loc: contains alignments of anchoring segments

       for global alignments with following format

       >seq1ID  seq2ID 
       1 start_pos    end_pos    score    sequence 
       2 start_pos    enc_pos    score    sequence

       For example,

       >seq1    seq2 
       1 557    777    100    ggggtgacgccctggccaggc...  
       2 141    361    100    gaggtgatatcccggacacgc...

   3) *.ACANA.score: contains the total alignment score of conserved 
       region and it includes total global alignment score for global alignment.

       The out format is given below:

       a) for global alignment 
      	 seq1ID   seq2ID  total_local_score total_global_score

       b) for local alignment only 
      	 seq1ID   seq2ID  total_local_score

    If no output filename specified, ACANA uses the input sequence filename 
    as the prefix of output filename and output files will be in the same.  
    directory of the input sequence file.  For example, if the input sequence 
    file is ./dir/SEQ.fa, then the output files are: 

   	(1) ./dir/SEQ.fa.ACANA 
    	(2) ./dir/SEQ.fa.ACANA.loc 
    	(3) ./dir/SEQ.fa.ACANA.score

OTHERS

    + ACANA is usually the  most accurate, but it uses much more memory than ACANA_L

    + ACANA2 runs a little bit faster and more memory efficient, but it may 
      be not as accuracy as the default ACANA program in aligning sequences 
      with high similarity but having many insertions or deletions.

ACKNOWLEDGE

    We would like to thank many users for their helpful feedbacks and bug reports  

==========
Contact: Weichun Huang at whduke@gmail.com
