Commit 3fc77ae6 authored by Alexis  CRISCUOLO's avatar Alexis CRISCUOLO

little editing

parent c88b51b0
......@@ -25,6 +25,6 @@ Distance-based approaches proceed in two steps: a pairwise evolutionary distance
In order to fill this void, the program *REQ* was developed. This tool estimates the rate of elementary quartets (REQ) for each branch of a given phylogenetic tree from the associated distance matrix, as described by [@guenoche2001]. This method simply computes the proportion of four-leaf subtrees (i.e. quartets) induced by every internal branch that are supported by the four-point condition applied to the six corresponding pairwise evolutionary distances [@zaretskii1965; @buneman1971]. Therefore, this measure is not based on a random sampling (such as bootstrap-based confidence supports). The closer this measure is to 1, the more the corresponding branch is fully supported by the pairwise evolutionary distances.
The program *REQ* is available on [GitLab](https://gitlab.pasteur.fr/GIPhy/REQ) under the [licence GNU GPLv3](https://www.gnu.org/licenses/gpl-3.0.en.html). Implemented in Java, *REQ* could be used on every operating system with a simple command line. *REQ* only needs two input files: a distance matrix file in either PHYLIP lower-triangular or square format, and a phylogenetic tree file in NEWICK format created from the distance matrix by any standard phylogenetic tree reconstruction method, e.g. neighbor-joining [@saitou1987; @studier1988], BioNJ [@gascuel1997], FastME [@desper2002]. Although computing the REQ value for every branch of a phylogenetic tree on *n* leaves requires *O*(*n*<sup>5</sup>) time complexity, *REQ* running time is quite fast (e.g. ~5 seconds with *n* = 500 on a standard computer) and could therefore be used with large phylogenetic trees.
The program *REQ* is available on [GitLab](https://gitlab.pasteur.fr/GIPhy/REQ) under the [licence GNU GPLv3](https://www.gnu.org/licenses/gpl-3.0.en.html). Implemented in Java, *REQ* could be used on every operating system with a simple command line. *REQ* only needs two input files: a distance matrix file in either PHYLIP lower-triangular or square format, and a phylogenetic tree file in NEWICK format created from the distance matrix by any standard phylogenetic tree reconstruction method, e.g. neighbor-joining [@saitou1987; @studier1988], BioNJ [@gascuel1997], FastME [@desper2002]. Although computing the REQ value for every branch of a phylogenetic tree on *n* leaves requires $O(n^5)$ time complexity, *REQ* running time is quite fast (e.g. ~5 seconds with *n* = 500 on a standard computer) and could therefore be used with large phylogenetic trees.
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