TREE-PUZZLE 

Input file name: ut-pure-prot.prot
User tree file name: ut-pure-prot.trees
Type of analysis: user tree evaluation
Parameter estimation: approximate (faster)
Parameter estimation uses: 1st user 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: 7 sequences with 128 amino acid sites
Number of constant sites: 7 (= 5.5% of all sites)
Number of site patterns: 125
Number of constant site patterns: 5 (= 4.0% of all site patterns)


SUBSTITUTION PROCESS

Model of substitution: Dayhoff (Dayhoff et al. 1978)
Amino acid frequencies (estimated from data set):

 pi(A) =  12.2%
 pi(R) =   2.3%
 pi(N) =   3.0%
 pi(D) =   4.9%
 pi(C) =   0.7%
 pi(Q) =   2.3%
 pi(E) =   5.4%
 pi(G) =   6.0%
 pi(H) =   5.8%
 pi(I) =   2.7%
 pi(L) =  12.5%
 pi(K) =   9.3%
 pi(M) =   1.3%
 pi(F) =   4.9%
 pi(P) =   2.6%
 pi(S) =   6.7%
 pi(T) =   4.5%
 pi(W) =   1.3%
 pi(Y) =   2.2%
 pi(V) =   9.4%


AMBIGUOUS CHARACTERS IN THE SEQUENCE (SEQUENCES IN INPUT ORDER)

               gaps  wildcards        sum   % sequence
 HBB_HUMAN        0          0          0        0.00%   
 HBB_HORSE        0          0          0        0.00%   
 HBA_HUMAN        0          0          0        0.00%   
 HBA_HORSE        0          0          0        0.00%   
 MYG_PHYCA        0          0          0        0.00%   
 GLB5_PETMA       0          0          0        0.00%   
 LGB2_LUPLU       0          0          0        0.00%   
 -------------------------------------------------------
 Sum              0          0          0        0.00%   


The table above shows the amount of gaps ('-') and other 'wildcard'
characters ('X', '?', etc.) and their percentage of the 128 columns
in the alignment.
Sequences with more than 50% ambiguous characters are marked with a '!' and 
should be checked, whether they have sufficient overlap to other sequences.
Sequences with 100% ambiguous characters do not hold any phylogenetic
information and had to be discarded from the analysis.



SEQUENCE COMPOSITION (SEQUENCES IN INPUT ORDER)

              5% chi-square test  p-value
 HBB_HUMAN         passed          92.31%  
 HBB_HORSE         passed          79.58%  
 HBA_HUMAN         passed          93.09%  
 HBA_HORSE         passed          81.20%  
 MYG_PHYCA         passed          33.23%  
 GLB5_PETMA        passed          19.11%  
 LGB2_LUPLU        passed          41.67%  

The chi-square tests compares the amino acid composition of each sequence
to the frequency distribution assumed in the maximum likelihood model.

WARNING: Result of chi-square test may not be valid because of small
maximum likelihood frequencies and short sequence length!


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.

  7
HBB_HUMAN   0.00000  0.17425  0.96068  0.99267  2.12932  1.77231  2.78644
HBB_HORSE   0.17425  0.00000  1.01062  1.02118  2.09456  1.78465  2.86187
HBA_HUMAN   0.96068  1.01062  0.00000  0.12147  1.93540  1.30123  2.54730
HBA_HORSE   0.99267  1.02118  0.12147  0.00000  2.00515  1.39193  2.51172
MYG_PHYCA   2.12932  2.09456  1.93540  2.00515  0.00000  2.12347  2.79386
GLB5_PETMA  1.77231  1.78465  1.30123  1.39193  2.12347  0.00000  2.18272
LGB2_LUPLU  2.78644  2.86187  2.54730  2.51172  2.79386  2.18272  0.00000

Average distance (over all possible pairs of sequences):  1.73823
                  minimum  : 0.12147,  maximum  : 2.86187
                  variance : 0.65214,  std.dev. : 0.80755


RATE HETEROGENEITY

Model of rate heterogeneity: uniform rate


TREE SEARCH

4 tree topologies were specified by the user.


MAXIMUM LIKELIHOOD BRANCH LENGTHS OF USER DEFINED TREE # 1 (NO CLOCK)

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


 :--2 HBB_HORSE
 :
 :            :-3 HBA_HUMAN
 :       :----8
 :       :    :-4 HBA_HORSE
 :------11
 :       :        :-------------5 MYG_PHYCA
 :       :     :--9
 :       :     :  :-------6 GLB5_PETMA
 :       :----10
 :             :-----------------7 LGB2_LUPLU
 :
 :-1 HBB_HUMAN
 

         branch  length     S.E.   branch  length     S.E.
HBB_HUMAN     1  0.04834  0.03148       8  0.28039  0.08746
HBB_HORSE     2  0.12686  0.03876       9  0.00001  0.00141
HBA_HUMAN     3  0.02653  0.02208      10  0.40361  0.12824
HBA_HORSE     4  0.09440  0.03145      11  0.60481  0.11282
MYG_PHYCA     5  1.33106  0.21114
GLB5_PETMA    6  0.70107  0.14140     9 iterations until convergence
LGB2_LUPLU    7  1.76830  0.28198     log L: -1699.50

WARNING --- at least one branch length is close to an internal boundary!


Unrooted user defined tree with maximum likelihood branch lengths
(in CLUSTAL W notation):

(HBB_HUMAN:0.04834,HBB_HORSE:0.12686,((HBA_HUMAN:0.02653,HBA_HORSE:0.09440)
:0.28039,((MYG_PHYCA:1.33106,GLB5_PETMA:0.70107):0.00001,LGB2_LUPLU:1.76830)
:0.40361):0.60481);


MAXIMUM LIKELIHOOD BRANCH LENGTHS OF USER DEFINED TREE # 2 (NO CLOCK)

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


 :--2 HBB_HORSE
 :
 :            :-3 HBA_HUMAN
 :       :----8
 :       :    :-4 HBA_HORSE
 :------11
 :       :     :-------------5 MYG_PHYCA
 :       :----10
 :             :   :------6 GLB5_PETMA
 :             :---9
 :                 :----------------7 LGB2_LUPLU
 :
 :-1 HBB_HUMAN
 

         branch  length     S.E.   branch  length     S.E.
HBB_HUMAN     1  0.04915  0.03158       8  0.28347  0.08778
HBB_HORSE     2  0.12604  0.03871       9  0.18149  0.13088
HBA_HUMAN     3  0.02555  0.02185      10  0.34695  0.12
HBA_HORSE     4  0.09541  0.03153      11  0.60238  0.11261
MYG_PHYCA     5  1.33157  0.21115
GLB5_PETMA    6  0.57473  0.13845     9 iterations until convergence
LGB2_LUPLU    7  1.71340  0.27647     log L: -1699.00


Unrooted user defined tree with maximum likelihood branch lengths
(in CLUSTAL W notation):

(HBB_HUMAN:0.04915,HBB_HORSE:0.12604,((HBA_HUMAN:0.02555,HBA_HORSE:0.09541)
:0.28347,(MYG_PHYCA:1.33157,(GLB5_PETMA:0.57473,LGB2_LUPLU:1.71340)
:0.18149):0.34695):0.60238);


MAXIMUM LIKELIHOOD BRANCH LENGTHS OF USER DEFINED TREE # 3 (NO CLOCK)

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


 :--2 HBB_HORSE
 :
 :            :-3 HBA_HUMAN
 :       :----8
 :       :    :-4 HBA_HORSE
 :------11
 :       :         :------------5 MYG_PHYCA
 :       :     :---9
 :       :     :   :----------------7 LGB2_LUPLU
 :       :----10
 :             :-------6 GLB5_PETMA
 :
 :-1 HBB_HUMAN
 

         branch  length     S.E.   branch  length     S.E.
HBB_HUMAN     1  0.04869  0.03153       8  0.27871  0.08717
HBB_HORSE     2  0.12653  0.03874       9  0.12334  0.15661
HBA_HUMAN     3  0.02634  0.02204      10  0.39110  0.12780
HBA_HORSE     4  0.09459  0.03147      11  0.60627  0.11286
MYG_PHYCA     5  1.22880  0.20960
GLB5_PETMA    6  0.69972  0.14141     11 iterations until convergence
LGB2_LUPLU    7  1.68480  0.28106     log L: -1699.32


Unrooted user defined tree with maximum likelihood branch lengths
(in CLUSTAL W notation):

(HBB_HUMAN:0.04869,HBB_HORSE:0.12653,((HBA_HUMAN:0.02634,HBA_HORSE:0.09459)
:0.27871,((MYG_PHYCA:1.22880,LGB2_LUPLU:1.68480):0.12334,GLB5_PETMA:0.69972)
:0.39110):0.60627);


MAXIMUM LIKELIHOOD BRANCH LENGTHS OF USER DEFINED TREE # 4 (NO CLOCK)

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


               :-------------5 MYG_PHYCA
         :-----8
         :     :-------6 GLB5_PETMA
         :     :
         :     :-----------------7 LGB2_LUPLU
 :------10
 :       :    :-3 HBA_HUMAN
 :       :----9
 :            :-4 HBA_HORSE
 :
 :--2 HBB_HORSE
 :
 :-1 HBB_HUMAN
 

         branch  length     S.E.   branch  length     S.E.
HBB_HUMAN     1  0.04834  0.03148       8  0.40364  0.12824
HBB_HORSE     2  0.12685  0.03876       9  0.28040  0.08746
HBA_HUMAN     3  0.02653  0.02208      10  0.60481  0.11281
HBA_HORSE     4  0.09440  0.03145
MYG_PHYCA     5  1.33095  0.21112
GLB5_PETMA    6  0.70107  0.14140     10 iterations until convergence
LGB2_LUPLU    7  1.76831  0.28198     log L: -1699.50


Unrooted user defined tree with maximum likelihood branch lengths
(in CLUSTAL W notation):

(HBB_HUMAN:0.04834,((MYG_PHYCA:1.33095,GLB5_PETMA:0.70107,LGB2_LUPLU:1.76831)
:0.40364,(HBA_HUMAN:0.02653,HBA_HORSE:0.09440):0.28040):0.60481,HBB_HORSE:0.12685);


COMPARISON OF USER TREES (NO CLOCK)

Tree   log L   difference    S.E.      p-1sKH     p-SH       c-ELW      2sKH
-------------------------------------------------------------------------------
 1   -1699.50     0.49      1.0266    0.3020 +   0.4700 +   0.1881 +       +
 2   -1699.00     0.00  <---- best    1.0000 +   1.0000 +   0.3650 +    best
 3   -1699.32     0.32      1.3440    0.4030 +   0.4690 +   0.2588 +       +
 4   -1699.50     0.49      1.0267    0.3070 +   0.4700 +   0.1881 +       +

The columns show the results and p-values of the following tests:
1sKH - one sided KH test based on pairwise SH tests (Shimodaira-Hasegawa
       2000, Goldman et al., 2001, Kishino-Hasegawa 1989)
SH   - Shimodaira-Hasegawa test (2000)
ELW  - Expected Likelihood Weight (Strimmer-Rambaut 2002)
2sKH - two sided Kishino-Hasegawa test (1989)

Plus signs denote the confidence sets. Minus signs denote significant
exclusion. All tests used 5% significance level. 1sKH, SH, and ELW
performed 1000 resamplings using the RELL method.
1sKH and 2sKH are correct to the 2nd position after the the decimal
point of the log-likelihoods.


TIME STAMP

