Amino acid substitution model
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Ancestral reconstruction
Ancestor gene reconstruction under constrains of amino acids
changes (Zhang and Nei 1997; Zhang et al., 1998)
First, Distance based Bayesian method applied for ancestral
proteins reconstruction, than parsimony applied for codons inference.
Universal genetic code only.
Amino acid substitution models:
LG (Le and Gascuel, 2008),
WAG (Whelan and Goldman, 2001),
JTT (Jones at al., 2001),
CpREV (Adachi et al., 2000),
MtREV (Adachi and Hasegawa, 1996),
MtZoa (Rota-Stabelli al., 2009).
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Correlation analysis
Phylogenetic statistic tests for evolutionary correlation
between molecular and phenotypical characteristics R: ape
You must enter quantitative phenotypical data for statistical analysis!
Methods for comparative analyses of data in a phylogenetic framework:
GEE (Paradis and Claude, 2002),
Lynch (Lynch, 1991),
Blomberg (Blomberg at al., 2003),
Martins (Martins and Hansen, 1997),
Grafen (Grafen, 1989),
Pagel (Pagel, 1999),
Brownian (Felsenstein, 1985).
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Format conversion
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Molecular clock analysis
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Multiple alignment
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Phylogeny reconstruction
A simple, fast, and accurate algorithm to estimate
large phylogenies by maximum likelihood approach (Guindon and Gascuel, 2003;
Quang et al, 2008)
Nucleotide substitution models:
GTR (Rodriguez et al., 1990),
HKY85 (Hasegawa et al., 1985),
K80 (Kimura, 1980),
JC69 (Jukes and Cantor, 1969),
F81 (Felsenstein, 1981),
F84 (Kishino and Hasegawa, 1989),
TN93 (Tamura and Nei, 1993).
Branch supports:
Approximate likelihood ratio (aLRT) and aLRT with Chi2 (Anisimova and Gascuel, 2006),
Shimodaira-Hasegawa (Shimodaira and Hasegawa, 1999).
Tree selection criteria:
Maximum-Likelihood (Aldrich, 1997).
Tree search algorithm:
Subtree pruning and regrafting (SPR) (Hordijk and Gascuel, 2005),
Nearest neighbor interchange (NNI).
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Radical to conservative amino acid replacement ratio
Calculation of Kr, Kc, Kr/Kc, and variances of Kr and Kc
(Zhang, 2000)
using all possible amino acid groupings in compliance with it's all
known physicochemical properties (Kawashima et al., 2008)
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Codeml_n -
Codeml (Yang, 2007) ancestor reconstruction under
various modification of M8 (Yang et al., 2000) codon evolution model,
Marginal reconstruction method (Koshi and Goldstein, 1996)
Input
Codon sequence gapless alignment in FASTA format
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Input
Unrooted tree in Newick format
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Genetic code
0 for the universal code, 1 for the mammalian mitochondrial code, 3 for mold mt, 4 for invertebrate mt, 5 for ciliate nuclear code, 6 for echinoderm mt, 7 for euplotid mt, 8 for alternative yeast nuclear, 9 for ascidian mt, and 10 for blepharisma nuclear
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Number of categories
Number of categories for beta and w codon substitution model (M8)
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Kappa (Ts/Tv) fixation
Kappa is fixed
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Kappa (Ts/Tv) parameter
Kappa (Ts/Tv) parameter (initial or fixed)
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Omega (Ka/Ks) fixation
Omega is fixed
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Omega (Ka/Ks) parameter
Omega (Ka/Ks) (initial or fixed)
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Codon frequencies in codon substitution model
Equal (0), Calculated from the average nucleotide frequencies (1), From the average nucleotide frequencies at the three codon positions (2), Used as free parameters (3)
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