Multiple sequence alignment program using Tree-based iterative algorithm 
for DNA.

    dapdp   : Similarity between each pair of sequences is estimated 
              with its pairwise alignment score obtained by DP.

    dmktree : Using a matrix of the similarity scores, UPGMA method 
              constructs a guided tree.

    dtria   : Tree-based round-robin iterative algorithm.

    dtpia_1 : Tree-based best-first iterative algorithm 
              with single-type partitioning.

    dtpia_2 : Tree-based best-first iterative algorithm 
              with double-type partitioning.

    dtpia_t : Tree-based best-first Iterative algorithm 
              with tree-dependent partitioning.


Usage 

(1) dtria|dtpia_1|dtpia_2|dtpia_t
 % dapdp    < datafile > apdp.out
 % program name [-a|-s]  < apdp.out  > result

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

-a : All result  
-s : Some result 

-----------------------------------------------------------------------------
The format of input data is shown as a example data file 'sample_dna.data'.
Plaese see an example  file 'sample_dna.data'.

------ input data format ----------------------------------------------------
U,V,S=7,1,1
CutP=80
CutM=90
MFlag=1
Same=-60
Diff=20

Seq=
CSRC (HUMAN):KLGQGCFGEVWMGTWNGTTRVAIKTLKPGTMSPEAFLQEAQVMKKLRHEKLV
CABL (HUMAN):KLGGGQYGEVYEGVWKKYSLTVAVKTLKEDTMEVEEFLKEAAVMKEIKHPNL
EPH (HUMAN):VIGEGEFGEVYRGTLRLPSQDCKTVAIKTLKDTSPGGQWWNFLREATIMGQFS
FER (HUMAN):LLGKGNFGEVYKGTLKDKTSVAVKTCKEDLPQELKIKFLQEAKILKQYDHPNI
IR (HUMAN):ELGQGSFGMVYEGNARDIIKGEAETRVAVKTVNESASLRERIEFLNEASVMKGF
CROS (HUMAN):LLGSGAFGEVYEGTAVDILGVGSGEIKVAVKTLKKGSTDQEKIEFLKEAHLM
TRK (HUMAN):ELGEGAFGKVFLAECHNLLPEQDKMLVAVKALKEASESARQDFQREAELLTML
BFGFR (HUMAN):PLGEGCFGQVVLAEAIGLDKDKPNRVTKVAVKMLKSDATEKDLSDLISEME
RET (HUMAN):TLGEGEFGKVVKATAFHLKGRAGYTTVAVKMLKENASPSELRDLLSEFNVLKQ
EGFR (HUMAN):VLGSGAFGTVYKGLWIPEGEKVKIPVAIKELREATSPKANKEILDEAYVMAS

-------------------------------------------------------------------
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 -------------------------------------------------
Our default parameter set is below.

 CutP=80
 CutM=97
 U,V,S=7,1,0

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



------ example of dapdp output  -----------------------------------------
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

CutP=80
CutM=90
U,V,S=40,5,5
Same=-60
Diff=20
MFlag=1

End of readSeq


ID1 ID2  L1  L1 Gap  AL     SC MCH EVT MCH-EVT
  0   1  49  44   5  49  -2375  41   4      37
  0   2  49  45   8  51  -2260  40   6      34
  0   3  49  49   0  49  -2060  38  11      27
  0   4  49  47  10  53  -2210  40   7      33
  0   5  49  46   5  50  -2195  40   8      32
  0   6  49  47  12  54  -2060  40   9      31
  0   7  49  45   4  49  -1800  34  12      22
  0   8  49  45   8  51  -1660  34  14      20
  0   9  49  47  26  61  -1050   0  46     -46
  0  10  49  47  22  59  -1190   0  46     -46
  0  11  49  45   4  49  -2240   0  47     -47
  0  12  49  49   2  50  -2430   0  50     -50
  0  13  49  47  22  59  -1190   0  47     -47
  0  14  49  45   6  50  -2290   0  47     -47
  0  15  49  47  22  59  -1190   0  46     -46
  1   2  44  45   1  45  -2075  37   8      29
  1   3  44  49   5  49  -1975  36   9      27
  1   4  44  47  11  51  -2105  38   6      32
  1   5  44  46   4  47  -2000  37  10      27
  1   6  44  47  13  52  -1635  33  11      22
  1   7  44  45   1  45  -1875  35  10      25
  1   8  44  45   9  49  -1755  35  10      25
  1   9  44  47  27  59  -1025   0  40     -40
  1  10  44  47  17  54  -1175   0  47     -47
  1  11  44  45   5  47  -2135   0  44     -44
  1  12  44  49   5  49  -2015   0  46     -46
  1  13  44  47  29  60  -1235   0  43     -43
  1  14  44  45   3  46  -2325   0  46     -46
  1  15  44  47  17  54  -1295   0  45     -45
  2   3  45  49  10  52  -1710  34  12      22
  2   4  45  47  10  51  -1730  34  12      22
  2   5  45  46   3  47  -2105  38   9      29
  2   6  45  47  10  51  -1850  35   9      26
  2   7  45  45   4  47  -1680  33  12      21
  2   8  45  45   2  46  -1750  34  12      22
  2   9  45  47  26  59   -970   0  45     -45
  2  10  45  47  18  55  -1090   0  45     -45
  2  11  45  45   4  47  -1880   0  45     -45
  2  12  45  49   4  49  -2000   0  47     -47
  2  13  45  47  20  56  -1220   0  46     -46
  2  14  45  45   2  46  -2150   0  46     -46
  2  15  45  47  20  56  -1180   0  46     -46
  3   4  49  47  16  56  -1880  37  10      27
  3   5  49  46  19  57  -1625  34  11      23
  3   6  49  47  14  55  -1830  37  11      26
  3   7  49  45   4  49  -2040  37   9      28
  3   8  49  45   6  50  -2050  38   9      29
  3   9  49  47  22  59  -1030   0  46     -46
  3  10  49  47  22  59  -1190   0  46     -46
  3  11  49  45   4  49  -2000   0  47     -47
  3  12  49  49   4  51  -1880   0  51     -51
  3  13  49  47  24  60  -1160   0  48     -48
  3  14  49  45   8  51  -1900   0  46     -46
  3  15  49  47  22  59  -1190   0  48     -48
  4   5  47  46   9  51  -1795  35  12      23
  4   6  47  47  12  53  -1920  37   9      28
  4   7  47  45   8  50  -1560  32  15      17
  4   8  47  45  18  55  -1410  31  14      17
  4   9  47  47  24  59  -1020   0  42     -42
  4  10  47  47  22  58  -1210   0  45     -45
  4  11  47  45  10  51  -1810   0  45     -45
  4  12  47  49   8  52  -1880   0  49     -49
  4  13  47  47  20  57  -1040   0  45     -45
  4  14  47  45  12  52  -1940   0  46     -46
  4  15  47  47  20  57  -1160   0  45     -45
  5   6  46  47   9  51  -1755  35  13      22
  5   7  46  45  13  52  -1755  35  11      24
  5   8  46  45   5  48  -1715  34  14      20
  5   9  46  47  29  61   -935   0  43     -43
  5  10  46  47  15  54  -1065   0  47     -47
  5  11  46  45   5  48  -1675   0  47     -47
  5  12  46  49   5  50  -1795   0  49     -49
  5  13  46  47  25  59   -955   0  42     -42
  5  14  46  45   5  48  -1875   0  48     -48
  5  15  46  47  17  55  -1075   0  48     -48
  6   7  47  45  18  55  -1490  32  12      20
  6   8  47  45   8  50  -1360  30  16      14
  6   9  47  47  34  64   -910   0  42     -42
  6  10  47  47  28  61  -1160   0  40     -40
  6  11  47  45   8  50  -1960   0  46     -46
  6  12  47  49  14  55  -1950   0  50     -50
  6  13  47  47  20  57  -1080   0  46     -46
  6  14  47  45  12  52  -1860   0  45     -45
  6  15  47  47  24  59  -1180   0  47     -47
  7   8  45  45   2  46  -2070  38   8      30
  7   9  45  47  26  59   -810   0  40     -40
  7  10  45  47  22  57   -910   0  46     -46
  7  11  45  45   4  47  -1960   0  45     -45
  7  12  45  49   6  50  -1770   0  48     -48
  7  13  45  47  22  57   -990   0  44     -44
  7  14  45  45   0  45  -1900   0  45     -45
  7  15  45  47  28  60   -980   0  45     -45
  8   9  45  47  20  56   -900   0  44     -44
  8  10  45  47  14  53   -990   0  47     -47
  8  11  45  45   6  48  -1730   0  46     -46
  8  12  45  49   4  49  -1560   0  48     -48
  8  13  45  47  28  60   -940   0  45     -45
  8  14  45  45   8  49  -1740   0  46     -46
  8  15  45  47  22  57   -990   0  45     -45
  9  10  47  47   6  50  -1810  35  13      22
  9  11  47  45  16  54  -1040  27  19       8
  9  12  47  49  16  56  -1080  28  21       7
  9  13  47  47  10  52  -1950  38  10      28
  9  14  47  45  26  59  -1170  28  13      15
  9  15  47  47  12  53  -1880  37  11      26
 10  11  47  45  16  54  -1240  30  18      12
 10  12  47  49  24  60  -1280  31  16      15
 10  13  47  47   6  50  -1970  37  11      26
 10  14  47  45  18  55  -1290  30  15      15
 10  15  47  47   4  49  -2200  39   8      31
 11  12  45  49   4  49  -2120  39   9      30
 11  13  45  47  22  57  -1190  29  15      14
 11  14  45  45   4  47  -2120  38   7      31
 11  15  45  47  16  54  -1200  29  18      11
 12  13  49  47  14  55  -1270  30  19      11
 12  14  49  45   4  49  -2160  39   8      31
 12  15  49  47  18  57  -1290  31  18      13
 13  14  47  45  16  54  -1440  32  14      18
 13  15  47  47   8  51  -2140  40   9      31
 14  15  45  47  18  55  -1370  31  15      16

END


---------------------------------------------------------------------------
(2)dmktree
 % dapdp   < datafile > dapdp.out
 % mktree  < dapdp.out

We use '../Module/matrix_dna.c' as a default matrix.
------ input data format ----------------------------------------------------
U,V,S=7,1,1
CutP=80
CutM=90
MFlag=1
Same=-60
Diff=20

Seq=
CSRC (HUMAN):KLGQGCFGEVWMGTWNGTTRVAIKTLKPGTMSPEAFLQEAQVMKKLRHEKLV
CABL (HUMAN):KLGGGQYGEVYEGVWKKYSLTVAVKTLKEDTMEVEEFLKEAAVMKEIKHPNL
EPH (HUMAN):VIGEGEFGEVYRGTLRLPSQDCKTVAIKTLKDTSPGGQWWNFLREATIMGQFS
FER (HUMAN):LLGKGNFGEVYKGTLKDKTSVAVKTCKEDLPQELKIKFLQEAKILKQYDHPNI
IR (HUMAN):ELGQGSFGMVYEGNARDIIKGEAETRVAVKTVNESASLRERIEFLNEASVMKGF
CROS (HUMAN):LLGSGAFGEVYEGTAVDILGVGSGEIKVAVKTLKKGSTDQEKIEFLKEAHLM
TRK (HUMAN):ELGEGAFGKVFLAECHNLLPEQDKMLVAVKALKEASESARQDFQREAELLTML
BFGFR (HUMAN):PLGEGCFGQVVLAEAIGLDKDKPNRVTKVAVKMLKSDATEKDLSDLISEME
RET (HUMAN):TLGEGEFGKVVKATAFHLKGRAGYTTVAVKMLKENASPSELRDLLSEFNVLKQ
EGFR (HUMAN):VLGSGAFGTVYKGLWIPEGEKVKIPVAIKELREATSPKANKEILDEAYVMAS
---------------------------------------------------------------------------

