Multiple Sequence Alignment Program for DNA


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We have three algorithms. We must choose one for our use.

 dist_dna [-f matrix] < data > dist

then

(1) align_dna 1 [-a,-s,-n] [-f matrix] < dist > result
(2) align_dna 2 [-a,-s,-n] [-f matrix] < dist > result
(3) align_dna 3 [-a,-s,-n] [-f matrix] < dist > result

(1)Tree-based Method
(2)Tree-based Round-robin Method
(3)Tree-based Round-robin Iterative Method

(1) aligns roughly but very fast.
(2) aligns well but needs times a little.
(3) aligns very well but needs times.

(3) is the best algolithm.
If your data is small or if you have enough time,please use it.

If your data is too big or if you don't have enough time,
please use (2).


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You can change a way of output by option [-a,-s,-n].

-a : All result  (Tree-based, round-robin and iterative result)
-s : Some result (Tree-based and round-robin result)
-n : Only final result


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You can also change a matrix by option [-f matrix].
The format of a matrix file is shown as a example matrix file 'matrix_example'.
Plaese see a example matrix file 'matrix_example'.
We use 'matrix_dna.c' as a default matrix.


------ input data format -----------------------------------------
CutM=80
CutI=90
U,V,S=40,5,5

Seq=
BTALULI1 1-250:ttaagttcagttcagtcactcagtcatgtccgactctttgcgaccccat
BTAAIIT1R 1838-2089:ttcagttcagttcagtcactcagtcgtgtccaactctttgcgac
BTACHRA1 2605-2853:accagttcaattcagtcgctcagtcatgtctgactctttgcgacc
BTALULI2 1-250:ttctgttcagtccagtggctcagttgtgtacaattctttgcaaccccat
OAKII9 1659-1906:tgggttgttgttcagtcactcagtcctgtgcaactctttgcgacccc
OAKERWL 2623-2875:aatgagtcagttcagtcactcagttatgtctgactctttgcgatct
BTAS1C 9410-9658:tgctgttgttcagtcgctcagtcatgcctgactctgtgaccccattg
OABCGLOB 2957-3200:ttcagtttagttcattggctcagttgtgtacgattctttgtgatc
OABBGLOB 3005-3249:ttcagttcacttcagtggctcagttgtgtatgatattttgcaatc
BTRPPST1 316-512:CAGCACACAAGGGTTCCCTGTCCATCACCAACACCCAGAGCTTCCTC
BTRPPST3 305-503:GCAGGACGCCAGGCCTCCCTGTCTATCACCAACTCCTGAGTCCACCC
CHGLOB01 4064-4316:TTCAGTTCAGTTCAGTCCCTCAGTCGTGTCCGATTCTGTGACCCC
OOGHOV 253-504:TTTAGTTCAGTTGCAGTTGCTCAGTCATGTCCGACTCCTTGGGACCCCA
BTRPPST4 297-497:TCACAGCATGCCAGGCGCCTGTCCATCACCAACTCCCAGAGTTCACC
BTCASK35 3650-3907:TTCAGTTCAGTTCAGTCGCTCAGTCATGTCCAACTCTTTCTGACC
BTRPPST2 307-506:CTGCAGCATGCCAGGTCTCCCTGTCCATCACCAACTCCTGAGTTTAC

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You must put a sequence data as "Sequence name:Sequence data"
or ":Sequence data". If no sequence name, ':' is necessary.
You must put return key at the end of sequence.


------ Parameters -------------------------------------------------
We have two best parameters sets.

(1) CutM=80       (2) CutM=85
    CutI=90           CutI=95
    U,V,S=40,5,5      U,V,S=40,5,5

U,V,S -> First Gap Cost -> U+V
         Not First Gap Cost -> V
         Out Gap Cost -> S

(1) is general
(2) is fast
