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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RenameSeq -
Rename sequence names in FASTA file and
save original names into separate file
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