User profiles for O. Gascuel
Olivier GascuelCNRS & Muséum National d'Histoire Naturelle Verified email at mnhn.fr Cited by 70995 |
Neighbor-joining revealed
… 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). …
be essentially equivalent to that of Saitou and Nei. Let f, g be the selected pair (fig. 1). …
New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0
… 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…
algorithm described above, starting from a BioNJ (Gascuel 1997) or a maximum parsimony (MP…
SeaView version 4: a multiplatform graphical user interface for sequence alignment and phylogenetic tree building
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 …
alignment and phylogenetic tree building from molecular sequence data through the use of a …
A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood
… 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 …
O(n)… This explains why our O(pns) ML optimization has computing time in the same range as …
Phylogeny. fr: robust phylogenetic analysis for the non-specialist
…, V Lefort, M Lescot, JM Claverie, O Gascuel - Nucleic acids …, 2008 - academic.oup.com
Phylogenetic analyses are central to many research areas in biology and typically involve
the identification of homologous sequences, their multiple alignment, the phylogenetic …
the identification of homologous sequences, their multiple alignment, the phylogenetic …
Approximate likelihood-ratio test for branches: a fast, accurate, and powerful alternative
M Anisimova, O Gascuel - Systematic biology, 2006 - academic.oup.com
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 …
data. A new, fast, approximate likelihood-ratio test (aLRT) for branches is presented here as a …
An improved general amino acid replacement matrix
… 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 …
search of the tree space (Hordijk and Gascuel 2005). The gamma shape parameter (α) and the …
BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data.
O Gascuel - Molecular biology and evolution, 1997 - academic.oup.com
… 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 …
the ordinary least-squares framework, ie, when we abandon the assumption of independence …
FastME 2.0: a comprehensive, accurate, and fast distance-based phylogeny inference program
V Lefort, R Desper, O Gascuel - Molecular biology and evolution, 2015 - academic.oup.com
… 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 …
taxa. The best SPR is selected and the procedure is iterated until no more improving SPR is …
PHYML Online—a web server for fast maximum likelihood-based phylogenetic inference
…, F Lethiec, P Duroux, O Gascuel - Nucleic acids …, 2005 - academic.oup.com
… 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 …
represents the number of refinement steps that have been performed and n is the number of …