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sylvia.phy_phyml_stats.txt
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oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
--- PhyML 20120412 ---
http://www.atgc-montpellier.fr/phyml
Copyright CNRS - Universite Montpellier II
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
. Sequence filename: sylvia.phy
. Data set: #1
. Tree topology search : NNIs
. Initial tree: BioNJ
. Model of nucleotides substitution: JC69
. Number of taxa: 25
. Log-likelihood: -9022.36183
. Unconstrained likelihood: -4483.83202
. Parsimony: 1376
. Tree size: 1.26926
. Nucleotides frequencies:
- f(A)= 0.25000
- f(C)= 0.25000
- f(G)= 0.25000
- f(T)= 0.25000
. Run ID: none
. Random seed: 1485536755
. Subtree patterns aliasing: no
. Version: 20120412
. Time used: 0h0m2s (2 seconds)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Suggested citations:
S. Guindon, JF. Dufayard, V. Lefort, M. Anisimova, W. Hordijk, O. Gascuel
"New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0."
Systematic Biology. 2010. 59(3):307-321.
S. Guindon & O. Gascuel
"A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood"
Systematic Biology. 2003. 52(5):696-704.
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
--- PhyML 20120412 ---
http://www.atgc-montpellier.fr/phyml
Copyright CNRS - Universite Montpellier II
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
. Sequence filename: sylvia.phy
. Data set: #1
. Tree topology search : NNIs
. Initial tree: BioNJ
. Model of nucleotides substitution: JC69
. Number of taxa: 25
. Log-likelihood: -8304.45208
. Unconstrained likelihood: -4483.83202
. Parsimony: 1378
. Tree size: 1.37832
. Proportion of invariant: 0.619
. Nucleotides frequencies:
- f(A)= 0.25000
- f(C)= 0.25000
- f(G)= 0.25000
- f(T)= 0.25000
. Run ID: none
. Random seed: 1485536757
. Subtree patterns aliasing: no
. Version: 20120412
. Time used: 0h0m2s (2 seconds)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Suggested citations:
S. Guindon, JF. Dufayard, V. Lefort, M. Anisimova, W. Hordijk, O. Gascuel
"New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0."
Systematic Biology. 2010. 59(3):307-321.
S. Guindon & O. Gascuel
"A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood"
Systematic Biology. 2003. 52(5):696-704.
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
--- PhyML 20120412 ---
http://www.atgc-montpellier.fr/phyml
Copyright CNRS - Universite Montpellier II
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
. Sequence filename: sylvia.phy
. Data set: #1
. Tree topology search : NNIs
. Initial tree: BioNJ
. Model of nucleotides substitution: JC69
. Number of taxa: 25
. Log-likelihood: -8229.36009
. Unconstrained likelihood: -4483.83202
. Parsimony: 1381
. Tree size: 1.49902
. Discrete gamma model: Yes
- Number of categories: 4
- Gamma shape parameter: 0.225
. Nucleotides frequencies:
- f(A)= 0.25000
- f(C)= 0.25000
- f(G)= 0.25000
- f(T)= 0.25000
. Run ID: none
. Random seed: 1485536759
. Subtree patterns aliasing: no
. Version: 20120412
. Time used: 0h0m7s (7 seconds)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Suggested citations:
S. Guindon, JF. Dufayard, V. Lefort, M. Anisimova, W. Hordijk, O. Gascuel
"New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0."
Systematic Biology. 2010. 59(3):307-321.
S. Guindon & O. Gascuel
"A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood"
Systematic Biology. 2003. 52(5):696-704.
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
--- PhyML 20120412 ---
http://www.atgc-montpellier.fr/phyml
Copyright CNRS - Universite Montpellier II
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
. Sequence filename: sylvia.phy
. Data set: #1
. Tree topology search : NNIs
. Initial tree: BioNJ
. Model of nucleotides substitution: JC69
. Number of taxa: 25
. Log-likelihood: -8215.18752
. Unconstrained likelihood: -4483.83202
. Parsimony: 1384
. Tree size: 1.46861
. Discrete gamma model: Yes
- Number of categories: 4
- Gamma shape parameter: 1.000
. Proportion of invariant: 0.513
. Nucleotides frequencies:
- f(A)= 0.25000
- f(C)= 0.25000
- f(G)= 0.25000
- f(T)= 0.25000
. Run ID: none
. Random seed: 1485536766
. Subtree patterns aliasing: no
. Version: 20120412
. Time used: 0h0m15s (15 seconds)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Suggested citations:
S. Guindon, JF. Dufayard, V. Lefort, M. Anisimova, W. Hordijk, O. Gascuel
"New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0."
Systematic Biology. 2010. 59(3):307-321.
S. Guindon & O. Gascuel
"A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood"
Systematic Biology. 2003. 52(5):696-704.
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
--- PhyML 20120412 ---
http://www.atgc-montpellier.fr/phyml
Copyright CNRS - Universite Montpellier II
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
. Sequence filename: sylvia.phy
. Data set: #1
. Tree topology search : NNIs
. Initial tree: BioNJ
. Model of nucleotides substitution: K80
. Number of taxa: 25
. Log-likelihood: -8508.62930
. Unconstrained likelihood: -4483.83202
. Parsimony: 1380
. Tree size: 1.29324
. Transition/transversion ratio: 6.512
. Nucleotides frequencies:
- f(A)= 0.25000
- f(C)= 0.25000
- f(G)= 0.25000
- f(T)= 0.25000
. Run ID: none
. Random seed: 1485536781
. Subtree patterns aliasing: no
. Version: 20120412
. Time used: 0h0m2s (2 seconds)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Suggested citations:
S. Guindon, JF. Dufayard, V. Lefort, M. Anisimova, W. Hordijk, O. Gascuel
"New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0."
Systematic Biology. 2010. 59(3):307-321.
S. Guindon & O. Gascuel
"A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood"
Systematic Biology. 2003. 52(5):696-704.
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
--- PhyML 20120412 ---
http://www.atgc-montpellier.fr/phyml
Copyright CNRS - Universite Montpellier II
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
. Sequence filename: sylvia.phy
. Data set: #1
. Tree topology search : NNIs
. Initial tree: BioNJ
. Model of nucleotides substitution: K80
. Number of taxa: 25
. Log-likelihood: -7778.21884
. Unconstrained likelihood: -4483.83202
. Parsimony: 1381
. Tree size: 1.44207
. Proportion of invariant: 0.620
. Transition/transversion ratio: 7.068
. Nucleotides frequencies:
- f(A)= 0.25000
- f(C)= 0.25000
- f(G)= 0.25000
- f(T)= 0.25000
. Run ID: none
. Random seed: 1485536783
. Subtree patterns aliasing: no
. Version: 20120412
. Time used: 0h0m5s (5 seconds)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Suggested citations:
S. Guindon, JF. Dufayard, V. Lefort, M. Anisimova, W. Hordijk, O. Gascuel
"New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0."
Systematic Biology. 2010. 59(3):307-321.
S. Guindon & O. Gascuel
"A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood"
Systematic Biology. 2003. 52(5):696-704.
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
--- PhyML 20120412 ---
http://www.atgc-montpellier.fr/phyml
Copyright CNRS - Universite Montpellier II
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
. Sequence filename: sylvia.phy
. Data set: #1
. Tree topology search : NNIs
. Initial tree: BioNJ
. Model of nucleotides substitution: K80
. Number of taxa: 25
. Log-likelihood: -7680.37478
. Unconstrained likelihood: -4483.83202
. Parsimony: 1380
. Tree size: 1.66984
. Discrete gamma model: Yes
- Number of categories: 4
- Gamma shape parameter: 0.222
. Transition/transversion ratio: 7.666
. Nucleotides frequencies:
- f(A)= 0.25000
- f(C)= 0.25000
- f(G)= 0.25000
- f(T)= 0.25000
. Run ID: none
. Random seed: 1485536788
. Subtree patterns aliasing: no
. Version: 20120412
. Time used: 0h0m7s (7 seconds)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Suggested citations:
S. Guindon, JF. Dufayard, V. Lefort, M. Anisimova, W. Hordijk, O. Gascuel
"New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0."
Systematic Biology. 2010. 59(3):307-321.
S. Guindon & O. Gascuel
"A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood"
Systematic Biology. 2003. 52(5):696-704.
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
--- PhyML 20120412 ---
http://www.atgc-montpellier.fr/phyml
Copyright CNRS - Universite Montpellier II
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
. Sequence filename: sylvia.phy
. Data set: #1
. Tree topology search : NNIs
. Initial tree: BioNJ
. Model of nucleotides substitution: K80
. Number of taxa: 25
. Log-likelihood: -7656.45797
. Unconstrained likelihood: -4483.83202
. Parsimony: 1382
. Tree size: 1.67626
. Discrete gamma model: Yes
- Number of categories: 4
- Gamma shape parameter: 0.852
. Proportion of invariant: 0.510
. Transition/transversion ratio: 7.939
. Nucleotides frequencies:
- f(A)= 0.25000
- f(C)= 0.25000
- f(G)= 0.25000
- f(T)= 0.25000
. Run ID: none
. Random seed: 1485536795
. Subtree patterns aliasing: no
. Version: 20120412
. Time used: 0h0m22s (22 seconds)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Suggested citations:
S. Guindon, JF. Dufayard, V. Lefort, M. Anisimova, W. Hordijk, O. Gascuel
"New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0."
Systematic Biology. 2010. 59(3):307-321.
S. Guindon & O. Gascuel
"A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood"
Systematic Biology. 2003. 52(5):696-704.
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
--- PhyML 20120412 ---
http://www.atgc-montpellier.fr/phyml
Copyright CNRS - Universite Montpellier II
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
. Sequence filename: sylvia.phy
. Data set: #1
. Tree topology search : NNIs
. Initial tree: BioNJ
. Model of nucleotides substitution: F81
. Number of taxa: 25
. Log-likelihood: -8938.16211
. Unconstrained likelihood: -4483.83202
. Parsimony: 1376
. Tree size: 1.27424
. Nucleotides frequencies:
- f(A)= 0.27006
- f(C)= 0.35371
- f(G)= 0.13108
- f(T)= 0.24515
. Run ID: none
. Random seed: 1485536817
. Subtree patterns aliasing: no
. Version: 20120412
. Time used: 0h0m2s (2 seconds)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Suggested citations:
S. Guindon, JF. Dufayard, V. Lefort, M. Anisimova, W. Hordijk, O. Gascuel
"New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0."
Systematic Biology. 2010. 59(3):307-321.
S. Guindon & O. Gascuel
"A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood"
Systematic Biology. 2003. 52(5):696-704.
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
--- PhyML 20120412 ---
http://www.atgc-montpellier.fr/phyml
Copyright CNRS - Universite Montpellier II
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
. Sequence filename: sylvia.phy
. Data set: #1
. Tree topology search : NNIs
. Initial tree: BioNJ
. Model of nucleotides substitution: F81
. Number of taxa: 25
. Log-likelihood: -8156.74503
. Unconstrained likelihood: -4483.83202
. Parsimony: 1380
. Tree size: 1.45833
. Proportion of invariant: 0.621
. Nucleotides frequencies:
- f(A)= 0.27006
- f(C)= 0.35371
- f(G)= 0.13108
- f(T)= 0.24515
. Run ID: none
. Random seed: 1485536819
. Subtree patterns aliasing: no
. Version: 20120412
. Time used: 0h0m2s (2 seconds)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Suggested citations:
S. Guindon, JF. Dufayard, V. Lefort, M. Anisimova, W. Hordijk, O. Gascuel
"New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0."
Systematic Biology. 2010. 59(3):307-321.
S. Guindon & O. Gascuel
"A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood"
Systematic Biology. 2003. 52(5):696-704.
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
--- PhyML 20120412 ---
http://www.atgc-montpellier.fr/phyml
Copyright CNRS - Universite Montpellier II
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
. Sequence filename: sylvia.phy
. Data set: #1
. Tree topology search : NNIs
. Initial tree: BioNJ
. Model of nucleotides substitution: F81
. Number of taxa: 25
. Log-likelihood: -8073.45386
. Unconstrained likelihood: -4483.83202
. Parsimony: 1379
. Tree size: 1.61180
. Discrete gamma model: Yes
- Number of categories: 4
- Gamma shape parameter: 0.212
. Nucleotides frequencies:
- f(A)= 0.27006
- f(C)= 0.35371
- f(G)= 0.13108
- f(T)= 0.24515
. Run ID: none
. Random seed: 1485536821
. Subtree patterns aliasing: no
. Version: 20120412
. Time used: 0h0m7s (7 seconds)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Suggested citations:
S. Guindon, JF. Dufayard, V. Lefort, M. Anisimova, W. Hordijk, O. Gascuel
"New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0."
Systematic Biology. 2010. 59(3):307-321.
S. Guindon & O. Gascuel
"A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood"
Systematic Biology. 2003. 52(5):696-704.
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
--- PhyML 20120412 ---
http://www.atgc-montpellier.fr/phyml
Copyright CNRS - Universite Montpellier II
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
. Sequence filename: sylvia.phy
. Data set: #1
. Tree topology search : NNIs
. Initial tree: BioNJ
. Model of nucleotides substitution: F81
. Number of taxa: 25
. Log-likelihood: -8058.00735
. Unconstrained likelihood: -4483.83202
. Parsimony: 1383
. Tree size: 1.60546
. Discrete gamma model: Yes
- Number of categories: 4
- Gamma shape parameter: 0.961
. Proportion of invariant: 0.523
. Nucleotides frequencies:
- f(A)= 0.27006
- f(C)= 0.35371
- f(G)= 0.13108
- f(T)= 0.24515
. Run ID: none
. Random seed: 1485536828
. Subtree patterns aliasing: no
. Version: 20120412
. Time used: 0h0m15s (15 seconds)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Suggested citations:
S. Guindon, JF. Dufayard, V. Lefort, M. Anisimova, W. Hordijk, O. Gascuel
"New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0."
Systematic Biology. 2010. 59(3):307-321.
S. Guindon & O. Gascuel
"A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood"
Systematic Biology. 2003. 52(5):696-704.
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
--- PhyML 20120412 ---
http://www.atgc-montpellier.fr/phyml
Copyright CNRS - Universite Montpellier II
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
. Sequence filename: sylvia.phy
. Data set: #1
. Tree topology search : NNIs
. Initial tree: BioNJ
. Model of nucleotides substitution: F84
. Number of taxa: 25
. Log-likelihood: -8470.40491
. Unconstrained likelihood: -4483.83202
. Parsimony: 1377
. Tree size: 1.29918
. Transition/transversion ratio: 6.610
. Nucleotides frequencies:
- f(A)= 0.27006
- f(C)= 0.35371
- f(G)= 0.13108
- f(T)= 0.24515
. Run ID: none
. Random seed: 1485536843
. Subtree patterns aliasing: no
. Version: 20120412
. Time used: 0h0m2s (2 seconds)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Suggested citations:
S. Guindon, JF. Dufayard, V. Lefort, M. Anisimova, W. Hordijk, O. Gascuel
"New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0."
Systematic Biology. 2010. 59(3):307-321.
S. Guindon & O. Gascuel
"A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood"
Systematic Biology. 2003. 52(5):696-704.
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
--- PhyML 20120412 ---
http://www.atgc-montpellier.fr/phyml
Copyright CNRS - Universite Montpellier II
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
. Sequence filename: sylvia.phy
. Data set: #1
. Tree topology search : NNIs
. Initial tree: BioNJ
. Model of nucleotides substitution: F84
. Number of taxa: 25
. Log-likelihood: -7612.86632
. Unconstrained likelihood: -4483.83202
. Parsimony: 1394
. Tree size: 1.66948
. Proportion of invariant: 0.623
. Transition/transversion ratio: 8.655
. Nucleotides frequencies:
- f(A)= 0.27006
- f(C)= 0.35371
- f(G)= 0.13108
- f(T)= 0.24515
. Run ID: none
. Random seed: 1485536845
. Subtree patterns aliasing: no
. Version: 20120412
. Time used: 0h0m2s (2 seconds)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Suggested citations:
S. Guindon, JF. Dufayard, V. Lefort, M. Anisimova, W. Hordijk, O. Gascuel
"New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0."
Systematic Biology. 2010. 59(3):307-321.
S. Guindon & O. Gascuel
"A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood"
Systematic Biology. 2003. 52(5):696-704.
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
--- PhyML 20120412 ---
http://www.atgc-montpellier.fr/phyml
Copyright CNRS - Universite Montpellier II
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
. Sequence filename: sylvia.phy
. Data set: #1
. Tree topology search : NNIs
. Initial tree: BioNJ
. Model of nucleotides substitution: F84
. Number of taxa: 25
. Log-likelihood: -7505.75871
. Unconstrained likelihood: -4483.83202
. Parsimony: 1380
. Tree size: 1.94739
. Discrete gamma model: Yes
- Number of categories: 4
- Gamma shape parameter: 0.194
. Transition/transversion ratio: 9.465
. Nucleotides frequencies:
- f(A)= 0.27006
- f(C)= 0.35371
- f(G)= 0.13108
- f(T)= 0.24515
. Run ID: none
. Random seed: 1485536847
. Subtree patterns aliasing: no
. Version: 20120412
. Time used: 0h0m8s (8 seconds)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Suggested citations:
S. Guindon, JF. Dufayard, V. Lefort, M. Anisimova, W. Hordijk, O. Gascuel
"New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0."
Systematic Biology. 2010. 59(3):307-321.
S. Guindon & O. Gascuel
"A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood"
Systematic Biology. 2003. 52(5):696-704.
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
--- PhyML 20120412 ---
http://www.atgc-montpellier.fr/phyml
Copyright CNRS - Universite Montpellier II
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
. Sequence filename: sylvia.phy
. Data set: #1
. Tree topology search : NNIs
. Initial tree: BioNJ
. Model of nucleotides substitution: F84
. Number of taxa: 25
. Log-likelihood: -7482.77363
. Unconstrained likelihood: -4483.83202
. Parsimony: 1382
. Tree size: 2.01977
. Discrete gamma model: Yes
- Number of categories: 4
- Gamma shape parameter: 0.820
. Proportion of invariant: 0.531
. Transition/transversion ratio: 9.966
. Nucleotides frequencies:
- f(A)= 0.27006
- f(C)= 0.35371
- f(G)= 0.13108
- f(T)= 0.24515
. Run ID: none
. Random seed: 1485536855
. Subtree patterns aliasing: no
. Version: 20120412
. Time used: 0h0m26s (26 seconds)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Suggested citations:
S. Guindon, JF. Dufayard, V. Lefort, M. Anisimova, W. Hordijk, O. Gascuel
"New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0."
Systematic Biology. 2010. 59(3):307-321.
S. Guindon & O. Gascuel
"A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood"
Systematic Biology. 2003. 52(5):696-704.
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
--- PhyML 20120412 ---
http://www.atgc-montpellier.fr/phyml
Copyright CNRS - Universite Montpellier II
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
. Sequence filename: sylvia.phy
. Data set: #1
. Tree topology search : NNIs
. Initial tree: BioNJ
. Model of nucleotides substitution: HKY85
. Number of taxa: 25
. Log-likelihood: -8429.87112
. Unconstrained likelihood: -4483.83202
. Parsimony: 1377
. Tree size: 1.30275
. Transition/transversion ratio: 6.408
. Nucleotides frequencies:
- f(A)= 0.27006
- f(C)= 0.35371
- f(G)= 0.13108
- f(T)= 0.24515
. Run ID: none
. Random seed: 1485536881
. Subtree patterns aliasing: no
. Version: 20120412
. Time used: 0h0m2s (2 seconds)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Suggested citations:
S. Guindon, JF. Dufayard, V. Lefort, M. Anisimova, W. Hordijk, O. Gascuel
"New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0."
Systematic Biology. 2010. 59(3):307-321.
S. Guindon & O. Gascuel
"A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood"
Systematic Biology. 2003. 52(5):696-704.
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
--- PhyML 20120412 ---
http://www.atgc-montpellier.fr/phyml
Copyright CNRS - Universite Montpellier II
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
. Sequence filename: sylvia.phy
. Data set: #1
. Tree topology search : NNIs
. Initial tree: BioNJ
. Model of nucleotides substitution: HKY85
. Number of taxa: 25
. Log-likelihood: -7587.34032
. Unconstrained likelihood: -4483.83202
. Parsimony: 1394
. Tree size: 1.65635
. Proportion of invariant: 0.621
. Transition/transversion ratio: 8.117
. Nucleotides frequencies:
- f(A)= 0.27006
- f(C)= 0.35371
- f(G)= 0.13108
- f(T)= 0.24515
. Run ID: none
. Random seed: 1485536883
. Subtree patterns aliasing: no
. Version: 20120412
. Time used: 0h0m3s (3 seconds)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Suggested citations:
S. Guindon, JF. Dufayard, V. Lefort, M. Anisimova, W. Hordijk, O. Gascuel
"New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0."
Systematic Biology. 2010. 59(3):307-321.
S. Guindon & O. Gascuel
"A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood"
Systematic Biology. 2003. 52(5):696-704.
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
--- PhyML 20120412 ---
http://www.atgc-montpellier.fr/phyml
Copyright CNRS - Universite Montpellier II
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
. Sequence filename: sylvia.phy
. Data set: #1
. Tree topology search : NNIs
. Initial tree: BioNJ
. Model of nucleotides substitution: HKY85
. Number of taxa: 25
. Log-likelihood: -7489.27179
. Unconstrained likelihood: -4483.83202
. Parsimony: 1380
. Tree size: 1.91817
. Discrete gamma model: Yes
- Number of categories: 4
- Gamma shape parameter: 0.198
. Transition/transversion ratio: 8.861
. Nucleotides frequencies:
- f(A)= 0.27006
- f(C)= 0.35371
- f(G)= 0.13108
- f(T)= 0.24515
. Run ID: none
. Random seed: 1485536886
. Subtree patterns aliasing: no
. Version: 20120412
. Time used: 0h0m7s (7 seconds)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Suggested citations:
S. Guindon, JF. Dufayard, V. Lefort, M. Anisimova, W. Hordijk, O. Gascuel
"New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0."
Systematic Biology. 2010. 59(3):307-321.
S. Guindon & O. Gascuel
"A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood"
Systematic Biology. 2003. 52(5):696-704.
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
--- PhyML 20120412 ---
http://www.atgc-montpellier.fr/phyml
Copyright CNRS - Universite Montpellier II
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
. Sequence filename: sylvia.phy
. Data set: #1
. Tree topology search : NNIs
. Initial tree: BioNJ
. Model of nucleotides substitution: HKY85
. Number of taxa: 25
. Log-likelihood: -7467.84201
. Unconstrained likelihood: -4483.83202
. Parsimony: 1382
. Tree size: 1.96774
. Discrete gamma model: Yes
- Number of categories: 4
- Gamma shape parameter: 0.856
. Proportion of invariant: 0.530
. Transition/transversion ratio: 9.296
. Nucleotides frequencies:
- f(A)= 0.27006
- f(C)= 0.35371
- f(G)= 0.13108
- f(T)= 0.24515
. Run ID: none
. Random seed: 1485536893
. Subtree patterns aliasing: no
. Version: 20120412
. Time used: 0h0m28s (28 seconds)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Suggested citations:
S. Guindon, JF. Dufayard, V. Lefort, M. Anisimova, W. Hordijk, O. Gascuel
"New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0."
Systematic Biology. 2010. 59(3):307-321.
S. Guindon & O. Gascuel
"A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood"
Systematic Biology. 2003. 52(5):696-704.
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
--- PhyML 20120412 ---
http://www.atgc-montpellier.fr/phyml
Copyright CNRS - Universite Montpellier II
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
. Sequence filename: sylvia.phy
. Data set: #1
. Tree topology search : NNIs
. Initial tree: BioNJ
. Model of nucleotides substitution: TN93
. Number of taxa: 25
. Log-likelihood: -8412.91731
. Unconstrained likelihood: -4483.83202
. Parsimony: 1377
. Tree size: 1.30746
. Transition/transversion ratio for purines: 4.636
. Transition/transversion ratio for pyrimidines: 7.168
. Nucleotides frequencies:
- f(A)= 0.27006
- f(C)= 0.35371
- f(G)= 0.13108
- f(T)= 0.24515
. Run ID: none
. Random seed: 1485536921
. Subtree patterns aliasing: no
. Version: 20120412
. Time used: 0h0m2s (2 seconds)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Suggested citations:
S. Guindon, JF. Dufayard, V. Lefort, M. Anisimova, W. Hordijk, O. Gascuel
"New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0."
Systematic Biology. 2010. 59(3):307-321.
S. Guindon & O. Gascuel
"A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood"
Systematic Biology. 2003. 52(5):696-704.
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
--- PhyML 20120412 ---
http://www.atgc-montpellier.fr/phyml
Copyright CNRS - Universite Montpellier II
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
. Sequence filename: sylvia.phy
. Data set: #1
. Tree topology search : NNIs
. Initial tree: BioNJ
. Model of nucleotides substitution: TN93
. Number of taxa: 25
. Log-likelihood: -7577.43350
. Unconstrained likelihood: -4483.83202
. Parsimony: 1386
. Tree size: 1.64242
. Proportion of invariant: 0.618
. Transition/transversion ratio for purines: 6.417
. Transition/transversion ratio for pyrimidines: 8.630
. Nucleotides frequencies:
- f(A)= 0.27006
- f(C)= 0.35371
- f(G)= 0.13108
- f(T)= 0.24515
. Run ID: none
. Random seed: 1485536923
. Subtree patterns aliasing: no
. Version: 20120412
. Time used: 0h0m2s (2 seconds)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Suggested citations:
S. Guindon, JF. Dufayard, V. Lefort, M. Anisimova, W. Hordijk, O. Gascuel
"New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0."
Systematic Biology. 2010. 59(3):307-321.
S. Guindon & O. Gascuel
"A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood"
Systematic Biology. 2003. 52(5):696-704.
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
--- PhyML 20120412 ---
http://www.atgc-montpellier.fr/phyml
Copyright CNRS - Universite Montpellier II
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
. Sequence filename: sylvia.phy
. Data set: #1
. Tree topology search : NNIs
. Initial tree: BioNJ
. Model of nucleotides substitution: TN93
. Number of taxa: 25
. Log-likelihood: -7483.68069
. Unconstrained likelihood: -4483.83202
. Parsimony: 1380
. Tree size: 1.95843
. Discrete gamma model: Yes
- Number of categories: 4
- Gamma shape parameter: 0.202
. Transition/transversion ratio for purines: 6.969
. Transition/transversion ratio for pyrimidines: 10.046
. Nucleotides frequencies:
- f(A)= 0.27006
- f(C)= 0.35371
- f(G)= 0.13108
- f(T)= 0.24515
. Run ID: none
. Random seed: 1485536925
. Subtree patterns aliasing: no
. Version: 20120412
. Time used: 0h0m9s (9 seconds)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Suggested citations:
S. Guindon, JF. Dufayard, V. Lefort, M. Anisimova, W. Hordijk, O. Gascuel
"New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0."
Systematic Biology. 2010. 59(3):307-321.
S. Guindon & O. Gascuel
"A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood"
Systematic Biology. 2003. 52(5):696-704.
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
--- PhyML 20120412 ---
http://www.atgc-montpellier.fr/phyml
Copyright CNRS - Universite Montpellier II
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
. Sequence filename: sylvia.phy
. Data set: #1
. Tree topology search : NNIs
. Initial tree: BioNJ
. Model of nucleotides substitution: TN93
. Number of taxa: 25
. Log-likelihood: -7461.59121
. Unconstrained likelihood: -4483.83202
. Parsimony: 1382
. Tree size: 1.99811
. Discrete gamma model: Yes
- Number of categories: 4
- Gamma shape parameter: 0.836
. Proportion of invariant: 0.523
. Transition/transversion ratio for purines: 7.079
. Transition/transversion ratio for pyrimidines: 10.788
. Nucleotides frequencies:
- f(A)= 0.27006
- f(C)= 0.35371
- f(G)= 0.13108
- f(T)= 0.24515
. Run ID: none
. Random seed: 1485536934
. Subtree patterns aliasing: no
. Version: 20120412
. Time used: 0h0m25s (25 seconds)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Suggested citations:
S. Guindon, JF. Dufayard, V. Lefort, M. Anisimova, W. Hordijk, O. Gascuel
"New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0."
Systematic Biology. 2010. 59(3):307-321.