… This formula is that of Studier and Keppler (1988), which we showed (Gascuel 1994) to
be essentially equivalent to that of Saitou and Nei. Let f, g be the selected pair (fig. 1). …

… Since the original publication (Guindon S., Gascuel O. 2003. A simple, fast and accurate …
algorithm described above, starting from a BioNJ (Gascuel 1997) or a maximum parsimony (MP…

We present SeaView version 4, a multiplatform program designed to facilitate multiple
alignment and phylogenetic tree building from molecular sequence data through the use of a …

… a requires O(s) time per branch and then O(ns) for the whole tree. Step b is fast, basically in
O(n)… This explains why our O(pns) ML optimization has computing time in the same range as …

Phylogenetic analyses are central to many research areas in biology and typically involve
the identification of homologous sequences, their multiple alignment, the phylogenetic …

We revisit statistical tests for branches of evolutionary trees reconstructed upon molecular
data. A new, fast, approximate likelihood-ratio test (aLRT) for branches is presented here as a …

… The starting tree is built by BIONJ (default option of PHYML), and we perform an SPR
search of the tree space (Hordijk and Gascuel 2005). The gamma shape parameter (α) and the …

… and we have shown (Gascuel 1997) that its use is well founded even when we abandon
the ordinary least-squares framework, ie, when we abandon the assumption of independence …

… We thus have O ( n 2 ) alternative trees to improve the initial tree, where n is the number of
taxa. The best SPR is selected and the procedure is iterated until no more improving SPR is …

… This explains the speed of this algorithm whose time complexity is O ( pns ), where p
represents the number of refinement steps that have been performed and n is the number of …