The following methods for reconstructing phylogenetic trees from a distance matrix containing missing values, i.e. incomplete matrices, are available: Triangles method by Guénoche and Leclerc (2001), Ultrametric procedure for the estimation of missing values by Landry, Lapointe and Kirsch (1996) followed by NJ, Additive procedure for the estimation of missing values by Landry, Lapointe and Kirsch (1996) followed by NJ, and the Modified Weighted least-squares method (MW*) by Makarenkov and Lapointe (2004).
The simulations described in (Makarenkov and Lapointe 2004) showed that the MW* method clearly outperforms the Triangles, Ultrametric and Additive procedures.
Complete and partial Horizontal gene transfer detection and validation methods are included in the T-REX server.
The following popular substitution models of DNA and amino acids evolution, allowing for estimating evolutionary distances from sequence data, have been included to T-REX: Uncorrected distance, Jukes-Cantor (Jukes and Cantor 1969), K80 – 2 parameters (Kimura 1980), T92 (Tamura 1992), Tajima-Nei (Tajima and Nei 1984), Jin-Nei gamma (Jin and Nei 1990), Kimura protein (Kimura 1983), LogDet (Lockhart et al. 1994), F84 (Felsenstein 1981), WAG (Whelan and Goldman 2001), JTT (Jones et al. 1992) and LG (Le and Gascuel 2008).
The branch lengths are multiplied by 1+ax, where the variable x is obtained from an exponential distribution (P(x>k) = exp(-k)), and the constant a is a tuning factor accounting for the deviation intensity (as described in Guindon and Gascuel (2002),[9] the value of a was set to 0.8).