INSTALLATION
    Just extract all files from ACANA_<System>.tar or ACANA_<System>.tgz or ACANA_<System>.zip
    to a directory by one of the following commands:
	tar xvf ACANA_<System>.tar
    	tar xvfz ACANA_<System>.tgz 
   	unzip ACANA_<System>.zip 
    
    Enter the directory ACANA_DIR, and follow the usage instructions below to run ACANA.
    
USEAGE

    Usage: ./ACANA -I InputSeqFile
    	   ./ACANA -I InputSeqFile -O outAlignfile.fa
    	   ./ACANA -I InputSeqFile -S ScoreMatrix -O outAlignfile.fa

    ========Required Parameters with Values========

    -I InputSeqFile Input sequence file in FASTA format

    ========Optional Parameters with Values========
    The default values are in brackets

    -S ScoreMatrix[dnaMatrix]    The scoring matrix file name  
    -O OutputFile                The output file name for alignments, see OUTPUT for the default value
    -G Open_Cost[-500]           The opening gap penalty
    -A Ext_Cost[-25]             The gap extension penalty
    -T ScoreFactor[10]           The factor used to increase the cutoff of local alignments
    -C CutOff_len[100]           The minimum length of anchoring segments

    ========Optional Indicator Parameters========

    -L Only output non-overlapping local alignments
    -P The input is protein sequences. The default is DNA sequences
    -H Print the usage information of ACANA
    -V Print the version information of ACANA

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
       format

    2) *.ACANA.loc: contains alignments of anchoring segments
       for global alignments with following format

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

       For example,
       >seq1    seq2   1616    -3179
       1 557    777    100    ggggtgacgccctggccaggc...
       2 141    361    100    gaggtgatatcccggacacgc...

    3) *.ACANA.score: contains the alignment score of conserved
       region and the score of a global alignment

    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 exmaple, 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 default program.
    + 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 an anonymous reviewer for his nice suggestions, 
    which has allowed me to make this instruction more complete and accurate. 

HISTORY
    ACANA_Fast was replaced by ACANA2. ACANA_Fast uses a constant gap cost
    model in local alignment process, while ACANA2 uses an affine gap cost
    model but uses a heuristic approach to improve alignment speed and 
    memory usage.

