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SUDI Example Outfile

Below is an example of a Phylip outfile. All unknown 
sequences need to be labeled U_seqID, where seqID represents 
the sequence name.  The outfile must be labeled as "OUTFILE"! 
The basenode for this examples is node 20.



  22 Populations

Neighbor-Joining/UPGMA method version 3.55c


 Neighbor-joining method

 Negative branch lengths allowed


                 +U_4057  
              +-12  
              !  !  +U_78    
              !  +-11  
              !     !  +U_P1795     
           +-15     +-10  
           !  !        +U_P2911     
           !  !  
           !  !     +-A_KE.Q231 
           !  !  +-13  
        +-16  +-14  +--A_SE.UGSE 
        !  !     !  
        !  !     +-A_UG.U455 
        !  !  
        !  !     +F1_DJ.DJ2 
        !  !  +--5  
     +-17  +--6  +F1_DJ.DJ2 
     !  !     !  
     !  !     +F2_NG.IBN 
     !  !  
     !  !     +-G_BE.DRCB 
     !  !  +--8  
     !  !  !  !  +-G_NG.92NG 
     !  +--9  +--7  
  +-19     !     +-G_SE.SE61 
  !  !     !  
  !  !     +-G_FI.HH87 
  !  !  
  !  !        +B_AU.MBC9 
  !  !     +--1  
  !  !  +--2  +B_CN.RL42 
  !  !  !  !  
  !  +-18  +-B_DE.HAN2 
  !     !  
  !     +---K_ZR.EQTB 
  !  
  !     +-C_BR.92BR 
  !  +--3  
-20--4  +-C_ET.ETH2 
  !  !  
  !  +C_BW.96BW 
  !  
  +-------------------OUTGROUP 


remember: (although rooted by outgroup) this is an unrooted tree!

Between        And            Length
-------        ---            ------
  20            19              0.00371
  19            17              0.00461
  17            16              0.01282
  16            15              0.00119
  15            12              0.02192
  12          U_4057          0.02254
  12            11              0.00028
  11          U_78            0.02137
  11            10              0.00203
  10          U_P1795             0.02057
  10          U_P2911             0.02033
  15            14              0.01099
  14            13              0.00293
  13          A_KE.Q231         0.03176
  13          A_SE.UGSE         0.03884
  14          A_UG.U455         0.03692
  16             6              0.02355
   6             5              0.00858
   5          I_DJ.DJ2         0.01597
   5          I_DJ.DJ2         0.00963
   6          I_NG.IBN         0.01732
  17             9              0.02420
   9             8              0.00187
   8          G_BE.DRCB         0.03366
   8             7              0.00084
   7          G_NG.92NG         0.02974
   7          G_SE.SE61         0.02886
   9          G_FI.HH87         0.02993
  19            18              0.00423
  18             2              0.03291
   2             1              0.00282
   1          B_AU.MBC9         0.01690
   1          B_CN.RL42         0.02260
   2          B_DE.HAN2         0.02098
  18          K_ZR.EQTB         0.06284
  20             4              0.02720
   4             3              0.00299
   3          C_BR.92BR         0.03458
   3          C_ET.ETH2         0.03492
   4          C_BW.96BW         0.02911
  20          OUTGROUP         0.33142


last modified: Wed Aug 8 16:35 2007


Questions or comments? Contact us at seq-info@lanl.gov.

 
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