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)


Concering parsimony informative sites there are:

Number of parsimony informative sites: 78 (= 60.9% of all sites)
  - fully informative sites:  12 (= 9.4% of all sites)
  - partly informative sites: 66 (= 51.6% of all sites)
Number of parsimony uninformative sites: 50 (= 39.1% of all sites)
  - variable, but uninformative sites: 43 (= 33.6% of all sites)
  - completely constant sites: 7 (= 5.5% of all sites)
  - constant sites (but with gaps/wildcards): 0 (= 0.0% of all sites)


For each sequence there are following numbers of parsimony (non-)informative site:

                    informative sites   non-informative sites
 1   HBB_HUMAN           72 ( 56.25%)            56 ( 43.75%)
 2   HBB_HORSE           75 ( 58.59%)            53 ( 41.41%)
 3   HBA_HUMAN           76 ( 59.38%)            52 ( 40.62%)
 4   HBA_HORSE           75 ( 58.59%)            53 ( 41.41%)
 5   MYG_PHYCA           41 ( 32.03%)            87 ( 67.97%)
 6   GLB5_PETMA          43 ( 33.59%)            85 ( 66.41%)
 7   LGB2_LUPLU          38 ( 29.69%)            90 ( 70.31%)

Note: partially informative sites are informative only for some sequences. Hence, the number of informative sites for each sequence can differ.


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
 1   HBB_HUMAN        0          0          0        0.00%   
 2   HBB_HORSE        0          0          0        0.00%   
 3   HBA_HUMAN        0          0          0        0.00%   
 4   HBA_HORSE        0          0          0        0.00%   
 5   MYG_PHYCA        0          0          0        0.00%   
 6   GLB5_PETMA       0          0          0        0.00%   
 7   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   chi2-value
 1   HBB_HUMAN         passed          92.31%     (11.02)  
 2   HBB_HORSE         passed          79.58%     (13.79)  
 3   HBA_HUMAN         passed          93.09%     (10.78)  
 4   HBA_HORSE         passed          81.20%     (13.50)  
 5   MYG_PHYCA         passed          33.23%     (21.08)  
 6   GLB5_PETMA        passed          19.11%     (24.13)  
 7   LGB2_LUPLU        passed          41.67%     (19.64)  

The chi-square tests with 19 degrees of freedom 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   0.00  0.17  0.96  0.99  2.12  1.77  2.78
HBB_HORSE   0.17  0.00  1.01  1.02  2.09  1.78  2.86
HBA_HUMAN   0.96  1.01  0.00  0.12  1.93  1.30  2.54
HBA_HORSE   0.99  1.02  0.12  0.00  2.00  1.39  2.51
MYG_PHYCA   2.12  2.09  1.93  2.00  0.00  2.12  2.79
GLB5_PETMA  1.77  1.78  1.30  1.39  2.12  0.00  2.18
LGB2_LUPLU  2.78  2.86  2.54  2.51  2.79  2.18  0.00

Average distance (over all possible pairs of sequences):  1.73
                  minimum  : 0.12,  maximum  : 2.86
                  variance : 0.65,  std.dev. : 0.80


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  0.04  0.03       8  0.28  0.08
HBB_HORSE     2  0.12  0.03       9  0.00  9.00
HBA_HUMAN     3  0.02  0.02      10  0.40  0.12
HBA_HORSE     4  0.09  0.03      11  0.60  0.11
MYG_PHYCA     5  1.33  0.21
GLB5_PETMA    6  0.70  0.14     9 iterations until convergence
LGB2_LUPLU    7  1.76  0.28     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:0.04,HBB_HORSE:0.12,((HBA_HUMAN:0.02,HBA_HORSE:0.09)
:0.28,((MYG_PHYCA:1.33,GLB5_PETMA:0.70):0.00,LGB2_LUPLU:1.76)
:0.40):0.60);


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  0.04  0.03       8  0.28  0.08
HBB_HORSE     2  0.12  0.03       9  0.18  0.13
HBA_HUMAN     3  0.02  0.02      10  0.34  0.12
HBA_HORSE     4  0.09  0.03      11  0.60  0.11
MYG_PHYCA     5  1.33  0.21
GLB5_PETMA    6  0.57  0.13     9 iterations until convergence
LGB2_LUPLU    7  1.71  0.27     log L: -1699.00


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

(HBB_HUMAN:0.04,HBB_HORSE:0.12,((HBA_HUMAN:0.02,HBA_HORSE:0.09)
:0.28,(MYG_PHYCA:1.33,(GLB5_PETMA:0.57,LGB2_LUPLU:1.71)
:0.18):0.34):0.60);


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  0.04  0.03       8  0.27  0.08
HBB_HORSE     2  0.12  0.03       9  0.12  0.15
HBA_HUMAN     3  0.02  0.02      10  0.39  0.12
HBA_HORSE     4  0.09  0.03      11  0.60  0.11
MYG_PHYCA     5  1.22  0.20
GLB5_PETMA    6  0.69  0.14     11 iterations until convergence
LGB2_LUPLU    7  1.68  0.28     log L: -1699.32


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

(HBB_HUMAN:0.04,HBB_HORSE:0.12,((HBA_HUMAN:0.02,HBA_HORSE:0.09)
:0.27,((MYG_PHYCA:1.22,LGB2_LUPLU:1.68):0.12,GLB5_PETMA:0.69)
:0.39):0.60);


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  0.04  0.03       8  0.40  0.12
HBB_HORSE     2  0.12  0.03       9  0.28  0.08
HBA_HUMAN     3  0.02  0.02      10  0.60  0.11
HBA_HORSE     4  0.09  0.03
MYG_PHYCA     5  1.33  0.21
GLB5_PETMA    6  0.70  0.14     10 iterations until convergence
LGB2_LUPLU    7  1.76  0.28     log L: -1699.50


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

(HBB_HUMAN:0.04,((MYG_PHYCA:1.33,GLB5_PETMA:0.70,LGB2_LUPLU:1.76)
:0.40,(HBA_HUMAN:0.02,HBA_HORSE:0.09):0.28):0.60,HBB_HORSE:0.12);


COMPARISON OF USER TREES (NO CLOCK)

Tree   log L   difference    S.E.      p-1sKH     p-SH       c-ELW      2sKH
-------------------------------------------------------------------------------
 1   -1699.50     0.49      1.02    0.31 +   0.46 +   0.18 +       +
 2   -1699.00     0.00  <---- best    1.00 +   1.00 +   0.36 +    best
 3   -1699.32     0.32      1.34    0.39 +   0.48 +   0.26 +       +
 4   -1699.50     0.49      1.02    0.33 +   0.46 +   0.18 +       +

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

