Commit d9f58626 authored by Alexis  CRISCUOLO's avatar Alexis CRISCUOLO

updating bib

parent 4661c570
@article{anisimova2006,
author = {Anisimova M and Gascuel O},
author = {Anisimova, M and Gascuel, O},
year = {2006},
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},
journal = {Molecular Biology and Evolution},
......@@ -129,8 +129,21 @@
url = {https://doi.org/10.1093/oxfordjournals.molbev.a025808}
}
@inproceedings{guenoche2001,
author = {Guénoche, A and Garreta, H},
year = {2001},
title = {Can we have confidence in a tree representation?},
booktitle= {Computational Biology},
editor = {Gascuel, O and Sagot, MF},
pages = {45--56},
publisher = {Springer Berlin Heidelberg},
address = {Berlin, Heidelberg},
doi = {10.1007/3-540-45727-5_5},
url = {http://iml.univ-mrs.fr/editions/biblio/guenoche/QualiTree-1.pdf}
}
@article{henz2005,
author = {Henz SR and Huson DH and Auch AF and Nieselt-Struwe K and Schuster SC},
author = {Henz, SR and Huson, DH and Auch, AF and Nieselt-Struwe, K and Schuster, SC},
year = {2005},
title = {Whole-genome prokaryotic phylogeny},
journal = {Bioinformatics},
......@@ -142,7 +155,7 @@
}
@article{hoang2018a,
author = {Hoang DT and Chernomor O and von Haeseler A and Minh BQ and Vinh LS},
author = {Hoang, DT and Chernomor, O and von Haeseler, A and Minh, BQ and Vinh, LS},
year = {2018},
title = {UFBoot2: improving the ultrafast bootstrap approximation},
journal = {Molecular Biology and Evolution},
......@@ -154,7 +167,7 @@
}
@article{hoang2018b,
author = {Hoang DY and Vinh LS and Flouri T and Stamatakis A and von Haeseler A and Minh BQ},
author = {Hoang, DY and Vinh, LS and Flouri, T and Stamatakis, A and von Haeseler, A and Minh, BQ},
year = {2018},
title = {MPBoot: fast phylogenetic maximum parsimony tree inference and bootstrap approximation},
journal = {BMC Evolutionary Biology},
......@@ -166,7 +179,7 @@
}
@article{house2014,
author = {House CH and Pellegrini M and Fitz-Gibbon ST},
author = {House, CH and Pellegrini, M and Fitz-Gibbon, ST},
year = {2014},
title = {Genome-wide gene order distances support clustering the gram-positive bacteria},
journal = {Frontiers in Microbiology},
......@@ -177,7 +190,7 @@
}
@article{krajewski1990,
author = {Krajewski C and Dickerman AW},
author = {Krajewski, C and Dickerman, AW},
year = {1990},
title = {Bootstrap analysis of phylogenetic trees derived from DNA hydridization distances},
journal = {Systematic Zoology},
......@@ -189,7 +202,7 @@
}
@article{lemoine2018,
author = {Lemoine F and Domelevo-Entfellner J-B and Wilkinson E and Correia D and Davila Felipe M and De Oliveira T and Gascuel O},
author = {Lemoine, F and Domelevo-Entfellner, J-B and Wilkinson, E and Correia, D and Davila Felipe, M and De Oliveira, T and Gascuel, O},
year = {2018},
title = {Renewing Felsenstein's phylogenetic bootstrap in the era of big data},
journal = {Nature},
......@@ -201,7 +214,7 @@
}
@article{makarenkov2010,
author = {Makarenkov V and Boc A and Xie J and Peres-Neto P and Lapointe F-J and Legendre P},
author = {Makarenkov, V and Boc, A and Xie, J and Peres-Neto, P and Lapointe, F-J and Legendre, P},
year = {2010},
title = {Weighted bootstrapping: a correction method for assessing the robustness of phylogenetic trees},
journal = {BMC Evolutionary Biology},
......@@ -212,7 +225,7 @@
}
@article{minh2013,
author = {Minh BQ and Nguyen MA and von Haeseler A},
author = {Minh, BQ and Nguyen, MA and von Haeseler, A},
year = {2013},
title = {Ultrafast approximation for phylogenetic bootstrap},
journal = {Molecular Biology and Evolution},
......@@ -224,7 +237,7 @@
}
@incollection{pardi2016,
author = {Pardi F and Gascuel O},
author = {Pardi, F and Gascuel, O},
year = {2016},
title = {Distance-based methods in phylogenetics},
booktitle = {Encyclopedia of Evolutionary Biology},
......@@ -235,7 +248,7 @@
}
@article{saitou1987,
author = {Saitou N and Nei M},
author = {Saitou, N and Nei, M},
year = {1987},
title = {The neighbor-joining method: a new method for reconstructing phylogenetic trees},
journal = {Molecular Biology and Evolution},
......@@ -247,7 +260,7 @@
}
@article{spencer2007,
author = {Spencer M and Bryant D and Susko E},
author = {Spencer, M and Bryant, D and Susko, E},
year = {2007},
title = {Conditioned genome reconstruction: how to avoid choosing the conditioning genome},
journal = {Systematic Biology},
......@@ -259,7 +272,7 @@
}
@article{studier1988,
author = {Studier JA and Kepler KJ},
author = {Studier, JA and Kepler, KJ},
year = {1988},
title = {A note on the neighbour-joining method of Saitou and Nei},
journal = {Molecular Biology and Evolution},
......@@ -271,7 +284,7 @@
}
@article{wang2006,
author = {Wang LS and Warnow T and Moret BM and Jansen RK and Raubeson LA},
author = {Wang, LS and Warnow, T and Moret, BM and Jansen, RK and Raubeson, LA},
year = {2006},
title = {Distance-based genome rearrangement phylogeny},
journal = {Journal of Molecular Evolution},
......@@ -283,10 +296,10 @@
}
@article{zaretskii1965,
author = {Zaretskii ZA},
author = {Zaretskii, ZA},
year = {1965},
title = {ПОСТРОЕНИЕ ДЕРЕВА ПО НАБОРУ РАССТОЯНИЙ МЕЖДУ ВИСЯЧИМИ ВЕРШИНАМИ},
note = {(Constructing a tree on the basis of a set of distances between the hanging vertices; in Russian)},
title = {Constructing a tree on the basis of a set of distances between the hanging vertices [in Russian]},
note = {ПОСТРОЕНИЕ ДЕРЕВА ПО НАБОРУ РАССТОЯНИЙ МЕЖДУ ВИСЯЧИМИ ВЕРШИНАМИ [real title]},
journal = {Uspekhi Matematicheskikh Nauk},
volume = {20},
number = {6},
......
......@@ -21,7 +21,7 @@ bibliography: paper.bib
*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.
......
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