Result file from the Puzzle program
PUZZLE (version 2.5.1)
Session of Sun Aug 24 12:03:20 1997
Runtime: 184 seconds (= 3.1 minutes = 0.1 hours)
MAXIMUM LIKELIHOOD MODEL
Sequence input data: 5 taxa with 166 amino acid sites
Model of sequence evolution: mtREV-22 (Adachi-Hasegawa 1995)
Amino acid frequencies (estimated from data set):
pi(A) = 1.7%
pi(R) = 1.5%
pi(N) = 3.2%
pi(D) = 4.8%
pi(C) = 5.4%
pi(Q) = 0.9%
pi(E) = 1.7%
pi(G) = 4.0%
pi(H) = 0.2%
pi(I) = 12.8%
pi(L) = 17.7%
pi(K) = 2.5%
pi(M) = 2.6%
pi(F) = 13.7%
pi(P) = 0.0%
pi(S) = 7.2%
pi(T) = 3.5%
pi(W) = 4.5%
pi(Y) = 5.1%
pi(V) = 7.1%
TREE SEARCH
Quartet puzzling is used to choose from the possible tree topologies
and to simultaneously infer reliability values for internal branches
Number of puzzling steps: 1000
Analysed quartets: 5
Unresolved quartets: 0 (= 0.0%)
Quartet trees are based on approximate maximum likelihood values
QUARTET PUZZLING TREE
* This is an unrooted tree
* Support for each internal branch is shown in percent
* The tree may be multifurcating
:---cox2_leita
:100:
:100: :---cox2_crifa
: :
: :-------cox2_trybb
:
:-----------Cox2_bsalt
:
:-----------cox2_tborr
Quartet puzzling tree (in CLUSTAL W notation):
(cox2_tborr,((cox2_leita,cox2_crifa)100,cox2_trybb)100,Cox2_bsalt);
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 consensus tree:
(bipartition with taxa in input order : number of times seen)
..*** : 1000
...** : 1000
Bipartitions not included in the consensus tree:
(bipartition with taxa in input order : number of times seen)
None (all bipartitions are included)
TAXA IN INPUT ORDER
cox2_leita
cox2_crifa
cox2_trybb
Cox2_bsalt
cox2_tborr
All taxa marked * differ on the basis of a 5% level chi-square test
in amino acid composition from the frequency distribution of
the maximum likelihood model
Warning: Result of chi-square test may be not valid because of small
maximum likelihood frequencies and short sequence length!
MAXIMUM LIKELIHOOD BRANCH LENGTHS ON QUARTET PUZZLING TREE
Branch lengths are computed using the selected model of
sequence evolution
:--1 cox2_leita
:---6
: :--2 cox2_crifa
:----7
: :---3 cox2_trybb
:
:--4 Cox2_bsalt
:
:-------------------5 cox2_tborr
num length +/- num length +/-
cox2_leita 1 0.0633 0.026 6 0.1047 0.036
cox2_crifa 2 0.0647 0.026 7 0.1479 0.048
cox2_trybb 3 0.1557 0.044
Cox2_bsalt 4 0.0760 0.038 8 iterations until convergence
cox2_tborr 5 1.1102 0.183 ln L: -950.73 +/- 59.58
Quartet puzzling tree with maximum likelihood branch lengths
(in CLUSTAL W notation):
(cox2_tborr:1.1102,((cox2_leita:0.0633,cox2_crifa:0.0647)100:0.1047,
cox2_trybb:0.1557)100:0.1479,Cox2_bsalt:0.0760);
MAXIMUM LIKELIHOOD DISTANCES
Maximum likelihood distances are computed using the selected model of
sequence evolution
5
cox2_leita 0.0000 0.1292 0.3171 0.4247 1.6361
cox2_crifa 0.1292 0.0000 0.3411 0.3575 1.6166
cox2_trybb 0.3171 0.3411 0.0000 0.4146 1.3554
Cox2_bsalt 0.4247 0.3575 0.4146 0.0000 1.2599
cox2_tborr 1.6361 1.6166 1.3554 1.2599 0.0000
Last updated: 25 August 1997.
created by :Fred
Opperdoes