Web document 7.9. Output of the TREE-PUZZLE program for 13 globin proteins.
TREE-PUZZLE 5.2
Input file name: 13globins.phy
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: 13 sequences with 170 amino acid sites
Number of constant sites: 4 (= 2.4% of all sites)
Number of site patterns: 168
Number of constant site patterns: 3 (= 1.8% of all site patterns)
SUBSTITUTION PROCESS
Model of substitution: Dayhoff (Dayhoff et al. 1978)
Amino acid frequencies (estimated from data set):
pi(A) =
12.0%
pi(R) =
2.1%
pi(N) =
2.8%
pi(D) =
5.8%
pi(C) =
0.6%
pi(Q) =
2.4%
pi(E) =
5.4%
pi(G) =
6.9%
pi(H) =
5.3%
pi(I) =
3.8%
pi(L) =
10.7%
pi(K) =
9.6%
pi(M) = 1.8%
pi(F) = 5.7%
pi(P) = 3.3%
pi(S) = 6.4%
pi(T) = 5.0%
pi(W) = 1.2%
pi(Y) = 1.9%
pi(V) = 7.5%
AMBIGUOUS CHARACTERS IN THE SEQUENCE (SEQUENCES IN INPUT ORDER)
gaps wildcards sum % sequence
mbkangaroo 16 0 16 9.41%
mbharbor_p 16 0 16 9.41%
mbgray_sea 16 0 16 9.41%
alphahorse 28 0 28 16.47%
alphakanga 29 0 29 17.06%
alphadog 29 0 29 17.06%
betadog 23 0 23 13.53%
betarabbit 23 0 23 13.53%
betakangar 24 0 24 14.12%
globinlamp 24 0 24 14.12%
globinseal 20 0 20 11.76%
globinsoyb 28 0 28 16.47%
globininse 19 0 19 11.18%
-------------------------------------------------------
Sum 295 0 295 13.35%
The table above shows the amount of gaps ('-') and other 'wildcard'
characters ('X', '?', etc.) and their percentage of the 170 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
mbkangaroo passed 26.80%
mbharbor_p passed 46.46%
mbgray_sea passed 48.39%
alphahorse passed 59.30%
alphakanga passed 92.71%
alphadog passed 23.85%
betadog passed 66.49%
betarabbit passed 53.16%
betakangar passed 82.28%
globinlamp passed 30.85%
globinseal passed 35.59%
globinsoyb passed 62.07%
globininse passed 25.92%
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.
13
mbkangaroo 0.00000 0.21902 0.20052 2.17425 2.12014 2.14530 2.00001
2.11096 2.14115 2.14558 2.10391 3.52637 2.48052
mbharbor_p 0.21902 0.00000 0.12093 2.07576 2.14874 2.02229 2.00365
2.14664 2.17650 2.32790 2.20266 3.57537 2.61353
mbgray_sea 0.20052 0.12093 0.00000 2.17915 2.16199 2.05370 1.99534
2.09580 2.17180 2.16355 2.10682 3.61475 2.64070
alphahorse 2.17425 2.07576 2.17915 0.00000 0.24644 0.21733 0.96849
0.92659 1.11683 1.57220 1.47385 2.44582 2.80913
alphakanga 2.12014 2.14874 2.16199 0.24644 0.00000 0.29110 1.02345
0.96551 1.06470 1.64357 1.57526 2.35081 2.97564
alphadog 2.14530 2.02229 2.05370 0.21733 0.29110 0.00000 1.04569
0.97727 1.13342 1.53262 1.50049 2.45586 2.94082
betadog 2.00001 2.00365 1.99534 0.96849 1.02345 1.04569 0.00000
0.15641 0.30774 1.66648 1.60807 2.59331 3.32967
betarabbit 2.11096 2.14664 2.09580 0.92659 0.96551 0.97727 0.15641
0.00000 0.31486 1.69085 1.67968 2.45026 3.26310
betakangar 2.14115 2.17650 2.17180 1.11683 1.06470 1.13342 0.30774
0.31486 0.00000 1.74675 1.68240 2.47610 3.33744
globinlamp 2.14558 2.32790 2.16355 1.57220 1.64357 1.53262 1.66648
1.69085 1.74675 0.00000 0.09023 2.48297 2.50849
globinseal 2.10391 2.20266 2.10682 1.47385 1.57526 1.50049 1.60807
1.67968 1.68240 0.09023 0.00000 2.62112 2.51371
globinsoyb 3.52637 3.57537 3.61475 2.44582 2.35081 2.45586 2.59331
2.45026 2.47610 2.48297 2.62112 0.00000 2.51450
globininse 2.48052 2.61353 2.64070 2.80913 2.97564 2.94082 3.32967
3.26310 3.33744 2.50849 2.51371 2.51450 0.00000
Average distance (over all possible pairs of sequences): 1.87503
minimum : 0.09023, maximum : 3.61475
variance : 0.78451, std.dev. : 0.88572
RATE HETEROGENEITY
Model of rate heterogeneity: uniform rate
QUARTET STATISTICS (SEQUENCES IN INPUT ORDER)
name | resolved | partly resolved | unresolved | sum
--------------------------------------------------------------------------
mbkangaroo 194 [ 88.18%] 3 [ 1.36%] 23 [ 10.45%] 220
mbharbor_p 196 [ 89.09%] 1 [ 0.45%] 23 [ 10.45%] 220
mbgray_sea 195 [ 88.64%] 3 [ 1.36%] 22 [ 10.00%] 220
alphahorse 200 [ 90.91%] 1 [ 0.45%] 19 [ 8.64%] 220
alphakanga 201 [ 91.36%] 1 [ 0.45%] 18 [ 8.18%] 220
alphadog 199 [ 90.45%] 2 [ 0.91%] 19 [ 8.64%] 220
betadog 199 [ 90.45%] 3 [ 1.36%] 18 [ 8.18%] 220
betarabbit 199 [ 90.45%] 4 [ 1.82%] 17 [ 7.73%] 220
betakangar 200 [ 90.91%] 4 [ 1.82%] 16 [ 7.27%] 220
globinlamp 200 [ 90.91%] 0 [ 0.00%] 20 [ 9.09%] 220
globinseal 201 [ 91.36%] 1 [ 0.45%] 18 [ 8.18%] 220
globinsoyb 157 [ 71.36%] 1 [ 0.45%] 62 [ 28.18%] 220
globininse 219 [ 99.55%] 0 [ 0.00%] 1 [ 0.45%] 220
--------------------------------------------------------------------------
#quartets : 640 [ 89.51%] 6 [ 0.84%] 69 [ 9.65%] 715
The table shows the occurrences of fully resolved, partially, and
completely unresolved quartets for each sequence and their percentage
relative to the number of times the sequence occurs in the list of
quartets (i.e. 220 quartets out of 715 in total).
In fully resolved quartet one single topology is supported, while for
partially resolved quartets two and for completely unresolved quartets
none of the topologies (AB||CD, AC||BD, AD||BC) are favoured.
Note: Because 4 sequences are involved in one quartet numbers add up
to a four-fold of the existing quartets.
Hint: The overall numbers in the last row give information about the
phylogenetic content of the dataset. The higher the percentage of partially
and unresolved quartets, the lower the content of phylogenetic information.
This can be visualized in more detail by likelihood mapping analysis.
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: 715
Fully resolved quartets: 640 (= 89.5%)
Partly resolved quartets: 6 (= 0.8%)
Unresolved quartets: 69 (= 9.7%)
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 completely resolved.
:---globinsoyb
:-------------95:
: :---globininse
:
: :---globinlamp
:100: :---------97:
: : : :---globinseal
: : :
: : : :---betadog
: :-62: :-89:
: : :100: :---betarabbit
: : : :
: : : :-------betakangar
: :-92:
: : :---alphahorse
: : :-76:
: :100: :---alphadog
: :
: :-------alphakanga
:
: :---mbharbor_p
:-----------------97:
: :---mbgray_sea
:
:-----------------------mbkangaroo
Quartet puzzling tree (in CLUSTAL W notation):
(mbkangaroo,((globinsoyb,globininse)95,((globinlamp,globinseal)97,
(((betadog,betarabbit)89,betakangar)100,((alphahorse,alphadog)76,
alphakanga)100)92)62)100,(mbharbor_p,mbgray_sea)97);
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
***...**** *** : 1000
***....... ... : 999
*********. .** : 973
*..******* *** : 972
********** *.. : 953
***......* *** : 915
******..** *** : 892
***.*.**** *** : 762
***....... .** : 623
Congruent bipartitions occurred in 50% or less, not included in
the consensus tree:
(bipartition with sequences in input order : number of times seen)
None (No congruent split not included)
Incongruent bipartitions not included in the consensus tree:
(bipartition with sequences in input order : number of times seen)
***..***** *** : 226
*********. ... : 219
***......* *.. : 152
*******..* *** : 102
***....... ..* : 29
***...***. ... : 24
***...**** *.. : 24
******.... ... : 20
*********. ..* : 18
******...* *.. : 17
*.*....... ... : 16
*********. *.. : 14
********** ... : 13
****..**** *** : 12
**........ ... : 12
******.*.* *** : 6
***...***. .** : 4
******.... .** : 2
*.*......* *.. : 1
MAXIMUM LIKELIHOOD BRANCH LENGTHS ON CONSENSUS TREE (NO CLOCK)
Branch lengths are computed using the selected model of
substitution and rate heterogeneity.
:---------12 globinsoyb
:----14
: :-----------13 globininse
:----------22
: : :-10 globinlamp
: : :-------15
: : : :-11 globinseal
: :-21
: : :-7 betadog
: : :-16
: : : :-8 betarabbit
: : :----17
: : : :--9 betakangar
: :---20
: : :-4 alphahorse
: : :-18
: : : :--6 alphadog
: :---19
: :-5 alphakanga
:
: :-2 mbharbor_p
:-23
: :-3 mbgray_sea
:
:-1 mbkangaroo
branch length S.E. branch length S.E.
mbkangaroo 1 0.07886 0.03279 14 0.53760 0.20175
mbharbor_p 2 0.07110 0.02354 15 0.81918 0.14939
mbgray_sea 3 0.04859 0.01981 16 0.05776 0.03282
alphahorse 4 0.08771 0.03069 17 0.47954 0.09621
alphakanga 5 0.10811 0.03530 18 0.06137 0.03158
alphadog 6 0.13950 0.03661 19 0.31739 0.08389
betadog 7 0.08054 0.02747 20 0.31729 0.11569
betarabbit 8 0.07571 0.02674 21 0.07578 0.12611
betakangar 9 0.18201 0.04507 22 1.28945 0.20094
globinlamp 10 0.07676 0.02490 23 0.07198 0.03259
globinseal 11 0.01386 0.01908
globinsoyb 12 1.16848 0.23708 20 iterations until convergence
globininse 13 1.40863 0.26701 log L: -2925.01
Consensus tree with maximum likelihood branch lengths
(in CLUSTAL W notation):
(mbkangaroo:0.07886,((globinsoyb:1.16848,globininse:1.40863)95:0.53760,
((globinlamp:0.07676,globinseal:0.01386)97:0.81918,(((betadog:0.08054,
betarabbit:0.07571)89:0.05776,betakangar:0.18201)100:0.47954,((
alphahorse:0.08771,alphadog:0.13950)76:0.06137,alphakanga:0.10811)
100:0.31739)92:0.31729)62:0.07578)100:1.28945,(mbharbor_p:0.07110,
mbgray_sea:0.04859)97:0.07198);
TIME STAMP
Date and time: Mon Aug 06 07:04:29 2007
Runtime (excl. input) : 4 seconds (= 0.1 minutes = 0.0 hours)
Runtime (incl. input) : 65 seconds (= 1.1 minutes = 0.0 hours)