Amino acid substitution model
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Ancestral reconstruction
Codeml (Yang, 2007) ancestor reconstruction under
various general and user defined substitution model,
Marginal reconstruction method (Koshi and Goldstein, 1996)
Amino acid substitution models:
LG (Le and Gascuel, 2008),
WAG (Whelan and Goldman, 2001),
JTT (Jones at al., 2001),
Dayhoff (Dayhoff et al., 1978),
DCMut (Kosiol and Goldman, 2005),
CpREV (Adachi et al., 2000),
MtREV (Adachi and Hasegawa, 1996),
MtMam (Cao et al., 1998),
MtArt (Abascal et al., 2007),
MtZoa (Rota-Stabelli al., 2009).
Fastml (Pupko et al., 2002) ancestor reconstruction
under various general substitution models,
Marginal reconstruction method (Koshi and Goldstein, 1996)
Amino acid substitution models:
LG (Le and Gascuel, 2008),
WAG (Whelan and Goldman, 2001),
JTT (Jones at al., 2001),
Dayhoff (Dayhoff et al., 1978),
CpREV (Adachi et al., 2000),
MtREV (Adachi and Hasegawa, 1996),
Jukes-Cantor (Jukes and Cantor, 1969).
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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)
Amino acid substitution models:
LG (Le and Gascuel, 2008),
WAG (Whelan and Goldman, 2001),
JTT (Jones at al., 2001),
Blosum62 (Henikoff and Henikoff, 1992),
Dayhoff (Dayhoff et al., 1978),
DCMut (Kosiol and Goldman, 2005),
VT (Muller and Vingron, 2000),
CpREV (Adachi et al., 2000),
MtREV (Adachi and Hasegawa, 1996),
RtREV (Dimmic et al., 2002),
MtMam (Cao et al., 1998),
MtArt (Abascal et al., 2007),
HIVw and HIVb (Dang et al., 2009),
Mixture Models (Le et al, 2008)
CAT model (Lartillot and Philippe, 2004).
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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Rare amino acid replacements
Detection of rare amino acid changes using comparison of
protein evolution model (INDELible: Fletcher and Yang, 2009)
with real data through nonparametric permutation test
(Gunbin et al., 2009)
Amino acid substitution models:
LG (Le and Gascuel, 2008),
WAG (Whelan and Goldman, 2001),
JTT (Jones at al., 2001),
Blosum (Henikoff and Henikoff, 1992),
Dayhoff (Dayhoff et al., 1978),
DCMut (Kosiol and Goldman, 2005),
VT (Muller and Vingron, 2000),
CpREV (Adachi et al., 2000),
MtREV (Adachi and Hasegawa, 1996),
RtREV (Dimmic et al., 2002),
MtMam (Cao et al., 1998),
MtArt (Abascal et al., 2007),
HIVw and HIVb (Dang et al., 2009).
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r8s -
(Sanderson, 2003). Constructing relaxed molecular clock
tree using Nonparametric rate smoothing - NPRS (Sanderson, 1997)
or Penalized likelihood, PL, approaches (Sanderson, 2002)
You must enter rooted tree for chronogram construction!
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