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

Ancescon (Cai et al., 2004) ancestor reconstruction under WAG substitution model (Whelan and Goldman, 2001), Marginal reconstruction method (Koshi and Goldstein, 1996)

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).

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

(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) CAT model (Lartillot and Philippe, 2004). 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) 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).

Summing up evolutionary changes Evolutionary distance corrections: Gamma (Ota and Nei, 1994), Kimura (Kimura, 1983), Jukes-Cantor (Jukes and Cantor, 1969).

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).