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 ...@@ -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. 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.
# References # References
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