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

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

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

    tree_based : Tree-based algorithm.
    tria_i1    : Tree-based round-robin algorithm.
    tria       : Tree-based round-robin iterative algorithm.

    tpia_1     : Tree-based best-first iterative algorithm 
                 with single-type partitioning.

    tpia_2     : Tree-based best-first iterative algorithm 
                 with double-type partitioning.

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

    tbm1as     : Tree-based random iterative algorithm 
                 with single-type partitioning.

    tbm2as     : Tree-based random iterative algorithm 
                 with double-type partitioning.

    tbmtas     : Tree-based random iterative algorithm 
                 with tree-dependent partitioning.


Usage 

(1)tree_based|tria_i1|tria|tpia_1|tpia_2|tpia_t|tbm1as|tbm2as|tbmtas
 % apdp   matrix_file  < datafile > apdp.out
 % program name [-a|-s]  [matrix file]  < apdp.out  > result

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

-a : All result  
-s : Some result 

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

------ input data format ----------------------------------------------------
U,V,S=7,1,1
CutP=80
CutM=97
MFlag=1

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

End of readSeq

-------------------------------------------------------------------
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.

 CutM=80
 U,V,S=7,1,1

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



------ example of apdp output  -----------------------------------------
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

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

End of readSeq


ID1 ID2  L1  L1 Gap  AL     SC MCH EVT MCH-EVT
  0   1  52  52   2  53   -138  27  26       1
  0   2  52  53  11  58    -71  20  30     -10
  0   3  52  53   5  55    -95  23  30      -7
  0   4  52  54  14  60    -76  22  28      -6
  0   5  52  52  18  61    -81  22  24      -2
  0   6  52  53  13  59    -63  16  34     -18
  0   7  52  51  17  60    -58  15  32     -17
  0   8  52  53  15  60    -58  18  30     -12
  0   9  52  52  16  60    -70  22  26      -4
  1   2  52  53   9  57    -90  19  32     -13
  1   3  52  53   5  55   -107  25  28      -3
  1   4  52  54  12  59    -83  23  27      -4
  1   5  52  52  16  60    -88  24  23       1
  1   6  52  53  11  58    -64  15  35     -20
  1   7  52  51  15  59    -38  18  32     -14
  1   8  52  53  15  60    -71  19  30     -11
  1   9  52  52  12  58    -96  21  28      -7
  2   3  53  53   8  57   -105  23  28      -5
  2   4  53  54   3  55    -92  18  36     -18
  2   5  53  52   9  57    -98  24  27      -3
  2   6  53  53   6  56    -88  21  33     -12
  2   7  53  51  12  58    -40  16  35     -19
  2   8  53  53   4  55    -92  18  36     -18
  2   9  53  52   5  55    -89  20  34     -14
  3   4  53  54  11  59    -99  22  28      -6
  3   5  53  52  15  60    -94  24  24       0
  3   6  53  53  12  59    -56  19  32     -13
  3   7  53  51   8  56    -36  11  41     -30
  3   8  53  53  14  60    -79  25  26      -1
  3   9  53  52  11  58    -73  18  31     -13
  4   5  54  52   4  55   -125  27  26       1
  4   6  54  53   1  54    -92  16  38     -22
  4   7  54  51   7  56    -62  16  36     -20
  4   8  54  53   3  55    -79  23  32      -9
  4   9  54  52   4  55    -82  22  33     -11
  5   6  52  53   5  55    -86  19  34     -15
  5   7  52  51   5  54    -70  17  35     -18
  5   8  52  53   3  54    -73  19  34     -15
  5   9  52  52  10  57    -97  23  27      -4
  6   7  53  51   8  56    -74  20  32     -12
  6   8  53  53   2  54    -69  23  31      -8
  6   9  53  52   9  57    -71  20  33     -13
  7   8  51  53   6  55    -99  26  26       0
  7   9  51  52  13  58    -46  16  34     -18
  8   9  53  52   1  53    -71  18  35     -17

END

---------------------------------------------------------------------------
(2)mktree
 % apdp  matrix_file < datafile > apdp.out
 % mktree [matrix_file] < apdp.out

About the format of matrix_file and datafile , please see (1).

---------------------------------------------------------------------------

