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codonphyml_stats.txt
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codonphyml_stats.txt
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# oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
# --- codonPhyML 1.00 201306.18 ---
# Marcelo S Zanetti
# Stefan Zoller
# Manuel Gil
# Louis du Plessis
# Maria Anisimova
# http://sourceforge.net/projects/codonphyml/
# oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
. Sequence filename: tmpwUVvFrphylip
. Data set: 1
. Tree topology search: NNIs
. Initial tree: BioNJ + GYECMK07
. Model name: GYECMK07+W+K+F F1x61
. Genetic code: Standard
. Number of taxa: 234
. Branch support: SH-like
. Log-likelihood: -24956.7
. Unconstrained Log-likelihood: -3552.21
. Parsimony: 77903
. Tree size: 8.01914
. Discrete gamma model: Yes
. Number of categories: 4
. Gamma shape (alpha): 0.443698
. Gamma shape (beta): 0.353292
. Proportion of invariant: 0
Emp. Transition/transverion ratio: ntv=0.24161504
Estimated dn/ds rate ratio (w) values: o0=0.00361262 p0=0.25000000 o1=0.03284750 p1=0.25000000 o2=0.11912032 p2=0.25000000 o3=0.45959352 p3=0.25000000
. Codon frequencies:
f(TTT)=0.01516527 f(TTC)=0.02002118 f(TTA)=0.01199607 f(TTG)=0.01907571
f(TCT)=0.01520309 f(TCC)=0.00992361 f(TCA)=0.02950609 f(TCG)=0.00193631
f(TAT)=0.02781938 f(TAC)=0.01907571 f(TAA)=0.00000000 f(TAG)=0.00000000
f(TGT)=0.01746464 f(TGC)=0.01024128 f(TGA)=0.00000000 f(TGG)=0.01840254
f(CTT)=0.00603585 f(CTC)=0.00543832 f(CTA)=0.02134483 f(CTG)=0.02148854
f(CCT)=0.00412979 f(CCC)=0.00791166 f(CCA)=0.01936313 f(CCG)=0.00306331
f(CAT)=0.01334241 f(CAC)=0.01115649 f(CAA)=0.01630739 f(CAG)=0.01180697
f(CGT)=0.00009076 f(CGC)=0.00001513 f(CGA)=0.00041600 f(CGG)=0.00037819
f(ATT)=0.02303154 f(ATC)=0.01330459 f(ATA)=0.02446108 f(ATG)=0.01540731
f(ACT)=0.01431813 f(ACC)=0.00655775 f(ACA)=0.03520157 f(ACG)=0.00472733
f(AAT)=0.04416459 f(AAC)=0.03545874 f(AAA)=0.04248544 f(AAG)=0.02406777
f(AGT)=0.01221541 f(AGC)=0.01443159 f(AGA)=0.02334922 f(AGG)=0.01123213
f(GTT)=0.01238182 f(GTC)=0.01366009 f(GTA)=0.01995310 f(GTG)=0.01556614
f(GCT)=0.01017321 f(GCC)=0.01591408 f(GCA)=0.02571666 f(GCG)=0.00515846
f(GAT)=0.02076999 f(GAC)=0.01804705 f(GAA)=0.04461841 f(GAG)=0.02077755
f(GGT)=0.01390969
. Time used: 2h12m10s
. Seconds: 7930
. MLTree: 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. MLTreeSize: 8.01914
#
# If you reconstruct trees or do model selection with CodonPhyML please cite:
# M. Gil, M.S. Zanetti, S. Zoller and M. Anisimova 2013
# CodonPhyML: Fast Maximum Likelihood Phylogeny Estimation under Codon Substitution Models
# Molecular Biology and Evolution, pages 1270-1280, volume 30, number 6
#
# If you use aBayes branch supports please cite:
# M. Anisimova, M. Gil, J.F. Dufayard, C. Dessimoz and O. Gascuel 2011
# Survey of branch support methods demonstrates accuracy, power, and robustness of fast likelihood-based approximation schemes. Syst Biol 60:685-699