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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SMITH-NEUTRAL -
Calculation of mean and standart
deviations of Kr, Kc, Kr/Kc (Smith, 2003) under neutral
evolution conditions (Ka/Ks=1) simulated by INDELible (Fletcher and Yang, 2009),
using all possible amino acid groupings in compliance with it's all
known physicochemical properties (Kawashima et al., 2008)
or using BLOSUM substitution matrix (Henikoff, Henikoff, 1992)
Input
FASTA gapless DNA alignment
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Input
Unrooted tree in Newick format
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Input
Tree in Newick format with ancestors labels
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Input
Legend file
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Input
Blosum MATRIX
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Input
Advanced clade model of evolution (INDELible format)
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Analysis type
On the basis of automatically generated model using PAML CODEML parameter estimation (auto); On the basis of user defined model (user)
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Ts/Tv
Transition transversion ratio (for simulation only): estimated by PAML CODEML (PAML), or user defined
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Iterations number
Iterations number
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Analyzing mode
BLOSUM matrix or ALL amino acid partitioning
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Amino acid partitioning
Number of amino acid classes
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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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