Amino acid substitution model estimation from alignment (Arvestad, 2006)

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).

Codeml (Yang, 2007) ancestor reconstruction under various modification of M8 (Yang et al., 2000) codon evolution model, Marginal reconstruction method (Koshi and Goldstein, 1996)

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).

Deleting gaps from alignment

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

Translate nucleic acid sequences into proteins (Rice et al., 2000)

Translate nucleic acid sequences into proteins (Rice et al., 2000)

(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!

Multiple sequence alignment algorithm designed to fast alignment of large numbers of protein sequences (Lassmann and Sonnhammer, 2005) Method references: Wu-Manber approximate string-matching algorithm (Wu and Manber, 1992), Dynamic programming (Eddy, 2004)

Accurate multiple sequence alignment algorithm based on fast Fourier transform (Katoh and Toh, 2008) with BLOSUM (Henikoff, Henikoff, 1992) or PAM (Dayhoff et al., 1978) or transmembrane PAM (Jones et al., 1994) matrices

Approximately Maximum-Likelihood Trees for Large Alignments (Price et al., 2010) GTR model (Rodriguez et al., 1990). Tree selection criteria: Minimum-Evolution (Rzhetsky and Nei, 1992), Maximum-Likelihood (Aldrich, 1997). Branch supports: Shimodaira-Hasegawa test (Shimodaira and Hasegawa, 1999), Bootstrap (Felsenstein, 1985). Tree search algorithm: Subtree pruning and regrafting (SPR) (Hordijk and Gascuel, 2005).

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).

Calculation of mean and standart deviations of Kr, Kc, Kr/Kc (Zhang, 2000) 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)

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)

Calculation of Kr, Kc, Kr/Kc (Smith, 2003) 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)

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)