title={Approximate likelihood-ratio test for branches: a fast, accurate, and powerful alternative},
journal={Systematic Biology},
...
...
@@ -11,7 +11,7 @@
}
@article{anisimova2011,
author={Anisimova M and Gil M and Dufayard J-F and Dessimoz C and Gascuel O},
author={Anisimova, M and Gil, M and Dufayard, J-F and Dessimoz, C and Gascuel, O},
year={2011},
title={Survey of branch support methods demonstrates accuracy, power, and robustness of fast likelihood-based approximation schemes},
journal={Systematic Biology},
...
...
@@ -23,7 +23,7 @@
}
@article{bremer1988,
author={Bremer K},
author={Bremer, K},
year={1988},
title={The limits of amino acid sequence data in angiosperm phylogenetic reconstruction},
journal={Evolution},
...
...
@@ -35,7 +35,7 @@
}
@article{bremer1994,
author={Bremer K},
author={Bremer, K},
year={1994},
title={Branch support and tree stability},
journal={Cladistics},
...
...
@@ -47,11 +47,11 @@
}
@inproceedings{buneman1971,
author={Buneman P},
author={Buneman, P},
year={1971},
title={The recovery of trees from measures of dissimilarity},
booktitle={Mathematics in Archaeological and Historical Sciences},
editor={Hodson FR and Kendall DG and Tautu P},
editor={Hodson, FR and Kendall, DG and Tautu, P},
pages={387--395},
publisher={Edinburgh University Press},
address={Edimburgh},
...
...
@@ -59,7 +59,7 @@
}
@article{chapus2005,
author={Chapus C and Dufraigne C and Edwards S and Giron A and Fertil B and Deschavanne PJ},
author={Chapus, C and Dufraigne, C and Edwards, S and Giron, A and Fertil, B and Deschavanne, PJ},
year={2005},
title={Exploration of phylogenetic data using a global sequence analysis method},
journal={BMC Evolutionary Biology},
...
...
@@ -70,7 +70,7 @@
}
@article{cohen2012,
author={Cohen E and Chor B},
author={Cohen, E and Chor, B},
year={2012},
title={Detecting phylogenetic signals in eukaryotic whole genome sequences},
journal={Journal of Computational Biology},
...
...
@@ -82,7 +82,7 @@
}
@article{desper2002,
author={Desper R and Gascuel O},
author={Desper, R and Gascuel, O},
year={2002},
title={Fast and accurate phylogeny reconstruction algorithms based on the minimum-evolution principle},
journal={Journal of Computational Biology},
...
...
@@ -94,7 +94,7 @@
}
@article{felsenstein1985,
author={Felsenstein J},
author={Felsenstein, J},
year={1985},
title={Confidence limits on phylogenies: an approach using the bootstrap},
journal={Evolution},
...
...
@@ -106,7 +106,7 @@
}
@article{garcia2018,
author={Garcia-Hermoso D and Criscuolo A and Lee SC and Legrand M and Chaouat M and Denis B and Lafaurie M and Rouveau M and Soler C and Schaal JV and Mimoun M and Mebazaa A and Heitman J and Dromer F and Brisse S and Bretagne S and Alanio A},
author={Garcia-Hermoso, D and Criscuolo, A and Lee, SC and Legrand, M and Chaouat, M and Denis, B and Lafaurie, M and Rouveau, M and Soler, C and Schaal, JV and Mimoun, M and Mebazaa, A and Heitman, J and Dromer, F and Brisse, S and Bretagne, S and Alanio, A},
year={2018},
title={Outbreak of invasive wound mucormycosis in a burn unit due to multiple strains of Mucor circinelloides f. circinelloides resolved by whole-genome sequencing},
journal={MBio},
...
...
@@ -118,7 +118,7 @@
}
@article{gascuel1997,
author={Gascuel O},
author={Gascuel, O},
year={1997},
title={BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data},
*REQ* is a program for quickly estimating a confidence value at each branch of a distance-based phylogenetic tree. Branch support assessment is commonly based on bootstrap procedures [@felsenstein1985; @makarenkov2010; @lemoine2018]. Unfortunately, as they are based on numerous resampling of aligned characters, such procedures require long running times, despite some recent advances [@minh2013; @hoang2018a; @hoang2018b]. In fact, direct branch support methods were already developed for character-based approaches that optimize maximum-parsimony or maximum-likelihood criteria, in order to achieve faster running times [@bremer1988; @bremer1994; @anisimova2006; @anisimova2011]. However, to our knowledge, no practical implementation of direct branch support methods is currently available for distance-based approaches.
Distance-based approaches proceed in two steps: a pairwise evolutionary distance is estimated between each pair of (biological) objects, and, next, an algorithm is used to infer the tree with branch lengths that best fits the evolutionary distance matrix [@pardi2016]. Because of their speed, distance-based methods are widely used for inferring phylogenetic trees. Moreover, as such algorithms only need a distance matrix, they allow phylogenetic analyses to be carried out from a wide range of data types, e.g. DNA-DNA hybridization experiments [krajewski1990], gene orders [@wang2006; @house2014], gene content [@spencer2007], or unaligned genome sequences [@chapus2005; @henz2005; @cohen2012; @garcia2018]. Nevertheless, in such cases, standard bootstrap-based methods can not be used for estimating branch confidence values.
Distance-based approaches proceed in two steps: a pairwise evolutionary distance is estimated between each pair of (biological) objects, and, next, an algorithm is used to infer the tree with branch lengths that best fits the evolutionary distance matrix [@pardi2016]. Because of their speed, distance-based methods are widely used for inferring phylogenetic trees. Moreover, as such algorithms only need a distance matrix, they allow phylogenetic analyses to be carried out from a wide range of data types, e.g. DNA-DNA hybridization experiments [@krajewski1990], gene orders [@wang2006; @house2014], gene content [@spencer2007], or unaligned genome sequences [@chapus2005; @henz2005; @cohen2012; @garcia2018]. Nevertheless, in such cases, standard bootstrap-based methods can not be used for estimating branch confidence values.
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.
