test5u.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

Quick add (only local branches initially optimized) in effect

User-supplied tree topology will be used.

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)

User-defined trees:


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

Remember: this is an unrooted tree!

Ln Likelihood =    -365.80850

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

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



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

Remember: this is an unrooted tree!

Ln Likelihood =    -374.57884

 Between        And             Length      Approx. Confidence Limits
 -------        ---             ------      ------- ---------- ------
   2          Sequence3         0.06867     (  0.01299,     0.13022) **
   2             1              0.00000     (     zero,     0.02880)
   1             3              0.14082     (  0.06276,     0.23097) **
   3          Sequence4         0.06155     (  0.01197,     0.11574) **
   3          Sequence5         0.02596     (     zero,     0.06481) **
   1          Sequence2         0.06268     (  0.00894,     0.12187) **
   2          Sequence1         0.14157     (  0.06516,     0.22951) **

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



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

Remember: this is an unrooted tree!

Ln Likelihood =    -372.26531

 Between        And             Length      Approx. Confidence Limits
 -------        ---             ------      ------- ---------- ------
   2          Sequence2         0.05076     (  0.00335,     0.10237) **
   2             1              0.02085     (     zero,     0.05426) *
   1             3              0.13281     (  0.05866,     0.21777) **
   3          Sequence4         0.05946     (  0.01021,     0.11325) **
   3          Sequence5         0.02831     (     zero,     0.06896) **
   1          Sequence3         0.05492     (  0.00578,     0.10858) **
   2          Sequence1         0.13541     (  0.06223,     0.21911) **

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



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

Remember: this is an unrooted tree!

Ln Likelihood =    -399.62271

 Between        And             Length      Approx. Confidence Limits
 -------        ---             ------      ------- ---------- ------
   1             2              0.01197     (     zero,     0.04296)
   2          Sequence2         0.11578     (  0.04568,     0.19547) **
   2          Sequence4         0.12038     (  0.04919,     0.20149) **
   1             3              0.00000     (     zero,     0.02449)
   3          Sequence3         0.10862     (  0.04249,     0.18322) **
   3          Sequence5         0.09735     (  0.03466,     0.16759) **
   1          Sequence1         0.10726     (  0.04319,     0.17925) **

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


Tree also written to treefile.24385

Tree      Ln L        Diff Ln L       Its S.D.   Significantly worse?

  1    -365.80850  <------ best
  2    -372.26531      -6.45680        6.6552            No
  3    -374.57884      -8.77033        5.3864            No
  4    -399.62271     -33.81420       11.7723           Yes