PUZZLE 4.0.2

Type of analysis: tree reconstruction
Parameter estimation: approximate (faster)
Parameter estimation uses: neighbor-joining tree (for substitution process and rate variation)

Standard errors (S.E.) are obtained by the curvature method.
The upper and lower bounds of an approximate 95% confidence interval
for parameter or branch length x are x-1.96*S.E. and x+1.96*S.E.


SEQUENCE ALIGNMENT

Input data: 12 sequences with 1376 nucleotide sites
Number of constant sites: 91 (= 6.6% of all sites)


SUBSTITUTION PROCESS

Model of substitution: HKY (Hasegawa et al. 1985)
Transition/transversion parameter (estimated from data set): 0.80 (S.E. 0.05)
Nucleotide frequencies (estimated from data set):

 pi(A) = 24.1%
 pi(C) = 26.4%
 pi(G) = 27.8%
 pi(T) = 21.6%

Expected transition/transversion ratio: 0.79
Expected pyrimidine transition/purine transition ratio: 0.85


RATE HETEROGENEITY

Model of rate heterogeneity: uniform rate


SEQUENCES IN INPUT ORDER

              5% chi-square test  p-value
 COW               failed         0.07%    [40] 
 FLY               passed         15.97%    [13] 
 CELEGANS          failed         0.00%    [3] 
 FLOWER            failed         0.00%    [12] 
 SOY               failed         3.43%    [16] 
 HOMO              failed         0.29%    [13] 
 PIG               passed         7.38%    [15] 
 MOUSE             passed         12.78%    [12] 
 RAT               passed         31.60%    [10] 
 TROUT             passed         72.15%    [14] 
 FROG              failed         0.03%    [8] 
 DANIO             passed         93.35%    [16] 

The chi-square tests compares the nucleotide composition of each sequence
to the frequency distribution assumed in the maximum likelihood model.
The number in square brackets indicates how often each sequence is
involved in one of the 43 completely unresolved quartets of the
quartet puzzling tree search.

IDENTICAL SEQUENCES

The sequences in each of the following groups are all identical. To speed
up computation please remove all but one of each group from the data set.

 All sequences are unique.


MAXIMUM LIKELIHOOD DISTANCES

Maximum likelihood distances are computed using the selected model of
substitution and rate heterogeneity.

  12
COW         0.00000  0.75211  0.78984  0.87832  0.89451  0.67213  0.62408
            0.64525  0.66083  0.62980  0.70988  0.67529
FLY         0.75211  0.00000  0.36466  0.44249  0.45519  0.39371  0.33199
            0.35416  0.36122  0.32351  0.40145  0.31724
CELEGANS    0.78984  0.36466  0.00000  0.44795  0.46567  0.43968  0.42498
            0.42498  0.44006  0.38730  0.41200  0.44470
FLOWER      0.87832  0.44249  0.44795  0.00000  0.24763  0.44715  0.43917
            0.45686  0.47905  0.42424  0.40220  0.44380
SOY         0.89451  0.45519  0.46567  0.24763  0.00000  0.43004  0.40784
            0.40775  0.44842  0.44009  0.45522  0.41448
HOMO        0.67213  0.39371  0.43968  0.44715  0.43004  0.00000  0.12102
            0.14814  0.15271  0.24709  0.25246  0.21784
PIG         0.62408  0.33199  0.42498  0.43917  0.40784  0.12102  0.00000
            0.13893  0.15519  0.20192  0.21830  0.20757
MOUSE       0.64525  0.35416  0.42498  0.45686  0.40775  0.14814  0.13893
            0.00000  0.04918  0.22245  0.24195  0.20246
RAT         0.66083  0.36122  0.44006  0.47905  0.44842  0.15271  0.15519
            0.04918  0.00000  0.23191  0.24801  0.22515
TROUT       0.62980  0.32351  0.38730  0.42424  0.44009  0.24709  0.20192
            0.22245  0.23191  0.00000  0.21392  0.15782
FROG        0.70988  0.40145  0.41200  0.40220  0.45522  0.25246  0.21830
            0.24195  0.24801  0.21392  0.00000  0.16610
DANIO       0.67529  0.31724  0.44470  0.44380  0.41448  0.21784  0.20757
            0.20246  0.22515  0.15782  0.16610  0.00000

Average distance (over all possible pairs of sequences):  0.39286


TREE SEARCH

Quartet puzzling is used to choose from the possible tree topologies
and to simultaneously infer support values for internal branches.

Number of puzzling steps: 1000
Analysed quartets: 495
Unresolved quartets: 43 (= 8.7%)

Quartet trees are based on approximate maximum likelihood values
using the selected model of substitution and rate heterogeneity.


QUARTET PUZZLING TREE

Support for the internal branches of the unrooted quartet puzzling
tree topology is shown in percent.

This quartet puzzling tree is not completely resolved!


         :---MOUSE     
     :100:             
     :   :---RAT       
 :-94:                 
 :   :   :---HOMO      
 :   :-91:             
 :       :---PIG       
 :                     
 :       :---FLOWER    
 :   :100:             
 :   :   :---SOY       
 :-90:                 
 :   :   :---FLY       
 :   :-58:             
 :       :---CELEGANS  
 :                     
 :       :---FROG      
 :   :-69:             
 :-58:   :---DANIO     
 :   :                 
 :   :-------TROUT     
 :                     
 :-----------COW       


Quartet puzzling tree (in CLUSTAL W notation):

(COW,((MOUSE,RAT)100,(HOMO,PIG)91)94,((FLOWER,SOY)100,(FLY,
CELEGANS)58)90,((FROG,DANIO)69,TROUT)58);


BIPARTITIONS

The following bipartitions occured at least once in all intermediate
trees that have been generated in the 1000 puzzling steps:

Bipartitions included in the quartet puzzling tree:
(bipartition with sequences in input order : number of times seen)

 *******..* **  :  1000
 ***..***** **  :  999
 *****....* **  :  941
 *****..*** **  :  913
 *....***** **  :  895
 ********** ..  :  685
 *..******* **  :  582
 *********. ..  :  575

Bipartitions not included in the quartet puzzling tree:
(bipartition with sequences in input order : number of times seen)

 *****..... ..  :  414
 **...***** **  :  372
 *........* ..  :  270
 *********. *.  :  261
 *........* **  :  235
 *....****. ..  :  204
 *****....* ..  :  125
 *....***** ..  :  75
 ***....... ..  :  69
 *****.*..* **  :  60
 *........* .*  :  44
 *.*....... ..  :  38
 *....***** .*  :  35
 *****..... **  :  30
 *....**... ..  :  21
 ******...* **  :  19
 *.***..... ..  :  17
 *.....*... ..  :  16
 *****..... *.  :  15
 *....****. **  :  11

(28 other less frequent bipartitions not shown)


MAXIMUM LIKELIHOOD BRANCH LENGTHS ON QUARTET PUZZLING TREE (NO CLOCK)

Branch lengths are computed using the selected model of
substitution and rate heterogeneity.


          :-8 MOUSE
      :--13
      :   :-9 RAT
 :---15
 :    :  :--6 HOMO
 :    :-14
 :       :--7 PIG
 :
 :            :----4 FLOWER
 :    :------16
 :    :       :----5 SOY
 :---18
 :    :   :-----2 FLY
 :    :--17
 :        :-------3 CELEGANS
 :
 :       :---11 FROG
 :   :--19
 :   :   :---12 DANIO
 :--20
 :   :---10 TROUT
 :
 :---------------1 COW
 

         branch  length     S.E.   branch  length     S.E.
COW           1  0.48425  0.03822      13  0.06028  0.01019
FLY           2  0.15103  0.01698      14  0.02106  0.00842
CELEGANS      3  0.23317  0.02235      15  0.07727  0.01243
FLOWER        4  0.11723  0.01479      16  0.18232  0.01920
SOY           5  0.13006  0.01507      17  0.04506  0.01296
HOMO          6  0.06653  0.01062      18  0.09042  0.01505
PIG           7  0.06575  0.01173      19  0.03943  0.01017
MOUSE         8  0.01681  0.00546      20  0.04182  0.01046
RAT           9  0.03296  0.00703
TROUT        10  0.09668  0.01311
FROG         11  0.09505  0.01309     8 iterations until convergence
DANIO        12  0.07435  0.01383     log L: -7862.04


Quartet puzzling tree with maximum likelihood branch lengths
(in CLUSTAL W notation):

(COW:0.48425,((MOUSE:0.01681,RAT:0.03296)100:0.06028,(HOMO:0.06653,
PIG:0.06575)91:0.02106)94:0.07727,((FLOWER:0.11723,SOY:0.13006)100:0.18232,
(FLY:0.15103,CELEGANS:0.23317)58:0.04506)90:0.09042,((FROG:0.09505,
DANIO:0.07435)69:0.03943,TROUT:0.09668)58:0.04182);


TIME STAMP

Date and time: Wed Jun 04 20:21:03 2003
Runtime: 10 seconds (= 0.2 minutes = 0.0 hours)