test5j.bst

fastDNAml is an attempt to solve the same problem as DNAML, but to do so faster and using less memo

fastDNAml, version 1.2.1, March 9, 1998

Based on Joseph Felsenstein's

   Nucleic acid sequence Maximum Likelihood method, version 3.3

5 Species, 114 Sites

Jumble random number seed = 137

Quick add (only local branches initially optimized) in effect

Rearrangements of partial trees may cross 1 branch.
Rearrangements of full tree may cross 1 branch.

Total weight of positions in analysis = 114
There are 41 distinct data patterns (columns)

Empirical Base Frequencies:

   A       0.18570
   C       0.24823
   G       0.31783
  T(U)     0.24823

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.571835)

Adding species:
   Sequence4
   Sequence2
   Sequence5
   Sequence1
      Tested 3 alternative trees
      Ln Likelihood =    -323.61247
   Sequence3
      Tested 5 alternative trees
      Ln Likelihood =    -365.80850
      Doing local rearrangements
      Tested 4 alternative trees

Examined 13 trees

                                   +----- Sequence5
   +-------------------------------1  
   !                               +------------------------- Sequence4
---2  
   !                         +------------------ Sequence2
   +-------------------------3  
   !                         +------------------------- Sequence3
   !  
   +------------------------------- Sequence1

Remember: this is an unrooted tree!

Ln Likelihood =    -365.80850

 Between        And             Length      Approx. Confidence Limits
 -------        ---             ------      ------- ---------- ------
   2             1              0.08775     (  0.02504,     0.15802) **
   1          Sequence5         0.01873     (     zero,     0.05038) *
   1          Sequence4         0.06742     (  0.01738,     0.12217) **
   2             3              0.06940     (  0.01393,     0.13070) **
   3          Sequence2         0.05346     (  0.00521,     0.10607) **
   3          Sequence3         0.06177     (  0.01061,     0.11786) **
   2          Sequence1         0.08289     (  0.02281,     0.14988) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Tree also written to treefile.24376