Commit c88b51b0 authored by Alexis  CRISCUOLO's avatar Alexis CRISCUOLO

updating bib

parent d9f58626
@article{anisimova2006, @article{anisimova2006,
author = {Anisimova, M and Gascuel, O}, author = {Anisimova, M. and Gascuel, O.},
year = {2006}, year = {2006},
title = {Approximate likelihood-ratio test for branches: a fast, accurate, and powerful alternative}, title = {Approximate likelihood-ratio test for branches: a fast, accurate, and powerful alternative},
journal = {Systematic Biology}, journal = {Systematic Biology},
...@@ -11,7 +11,7 @@ ...@@ -11,7 +11,7 @@
} }
@article{anisimova2011, @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}, year = {2011},
title = {Survey of branch support methods demonstrates accuracy, power, and robustness of fast likelihood-based approximation schemes}, title = {Survey of branch support methods demonstrates accuracy, power, and robustness of fast likelihood-based approximation schemes},
journal = {Systematic Biology}, journal = {Systematic Biology},
...@@ -23,7 +23,7 @@ ...@@ -23,7 +23,7 @@
} }
@article{bremer1988, @article{bremer1988,
author = {Bremer, K}, author = {Bremer, K.},
year = {1988}, year = {1988},
title = {The limits of amino acid sequence data in angiosperm phylogenetic reconstruction}, title = {The limits of amino acid sequence data in angiosperm phylogenetic reconstruction},
journal = {Evolution}, journal = {Evolution},
...@@ -35,7 +35,7 @@ ...@@ -35,7 +35,7 @@
} }
@article{bremer1994, @article{bremer1994,
author = {Bremer, K}, author = {Bremer, K.},
year = {1994}, year = {1994},
title = {Branch support and tree stability}, title = {Branch support and tree stability},
journal = {Cladistics}, journal = {Cladistics},
...@@ -47,11 +47,11 @@ ...@@ -47,11 +47,11 @@
} }
@inproceedings{buneman1971, @inproceedings{buneman1971,
author = {Buneman, P}, author = {Buneman, P.},
year = {1971}, year = {1971},
title = {The recovery of trees from measures of dissimilarity}, title = {The recovery of trees from measures of dissimilarity},
booktitle= {Mathematics in Archaeological and Historical Sciences}, booktitle= {Mathematics in Archaeological and Historical Sciences},
editor = {Hodson, FR and Kendall, DG and Tautu, P}, editor = {Hodson, F.~R. and Kendall, D.~G. and Tautu, P.},
pages = {387--395}, pages = {387--395},
publisher = {Edinburgh University Press}, publisher = {Edinburgh University Press},
address = {Edimburgh}, address = {Edimburgh},
...@@ -59,7 +59,7 @@ ...@@ -59,7 +59,7 @@
} }
@article{chapus2005, @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, P.~J.},
year = {2005}, year = {2005},
title = {Exploration of phylogenetic data using a global sequence analysis method}, title = {Exploration of phylogenetic data using a global sequence analysis method},
journal = {BMC Evolutionary Biology}, journal = {BMC Evolutionary Biology},
...@@ -70,7 +70,7 @@ ...@@ -70,7 +70,7 @@
} }
@article{cohen2012, @article{cohen2012,
author = {Cohen, E and Chor, B}, author = {Cohen, E. and Chor, B.},
year = {2012}, year = {2012},
title = {Detecting phylogenetic signals in eukaryotic whole genome sequences}, title = {Detecting phylogenetic signals in eukaryotic whole genome sequences},
journal = {Journal of Computational Biology}, journal = {Journal of Computational Biology},
...@@ -82,7 +82,7 @@ ...@@ -82,7 +82,7 @@
} }
@article{desper2002, @article{desper2002,
author = {Desper, R and Gascuel, O}, author = {Desper, R. and Gascuel, O.},
year = {2002}, year = {2002},
title = {Fast and accurate phylogeny reconstruction algorithms based on the minimum-evolution principle}, title = {Fast and accurate phylogeny reconstruction algorithms based on the minimum-evolution principle},
journal = {Journal of Computational Biology}, journal = {Journal of Computational Biology},
...@@ -94,7 +94,7 @@ ...@@ -94,7 +94,7 @@
} }
@article{felsenstein1985, @article{felsenstein1985,
author = {Felsenstein, J}, author = {Felsenstein, J.},
year = {1985}, year = {1985},
title = {Confidence limits on phylogenies: an approach using the bootstrap}, title = {Confidence limits on phylogenies: an approach using the bootstrap},
journal = {Evolution}, journal = {Evolution},
...@@ -106,7 +106,7 @@ ...@@ -106,7 +106,7 @@
} }
@article{garcia2018, @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, S.~C. and Legrand, M. and Chaouat, M. and Denis, B. and Lafaurie, M. and Rouveau, M. and Soler, C. and Schaal, J.~V. and Mimoun, M. and Mebazaa, A. and Heitman, J. and Dromer, F. and Brisse, S. and Bretagne, S. and Alanio, A.},
year = {2018}, 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}, 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}, journal = {MBio},
...@@ -118,7 +118,7 @@ ...@@ -118,7 +118,7 @@
} }
@article{gascuel1997, @article{gascuel1997,
author = {Gascuel, O}, author = {Gascuel, O.},
year = {1997}, year = {1997},
title = {BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data}, title = {BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data},
journal = {Molecular Biology and Evolution}, journal = {Molecular Biology and Evolution},
...@@ -130,11 +130,11 @@ ...@@ -130,11 +130,11 @@
} }
@inproceedings{guenoche2001, @inproceedings{guenoche2001,
author = {Guénoche, A and Garreta, H}, author = {Guénoche, A. and Garreta, H.},
year = {2001}, year = {2001},
title = {Can we have confidence in a tree representation?}, title = {Can we have confidence in a tree representation?},
booktitle= {Computational Biology}, booktitle= {Computational Biology},
editor = {Gascuel, O and Sagot, MF}, editor = {Gascuel, O. and Sagot, M.-F.},
pages = {45--56}, pages = {45--56},
publisher = {Springer Berlin Heidelberg}, publisher = {Springer Berlin Heidelberg},
address = {Berlin, Heidelberg}, address = {Berlin, Heidelberg},
...@@ -143,7 +143,7 @@ ...@@ -143,7 +143,7 @@
} }
@article{henz2005, @article{henz2005,
author = {Henz, SR and Huson, DH and Auch, AF and Nieselt-Struwe, K and Schuster, SC}, author = {Henz, S.~R. and Huson, D.~H. and Auch, A.~F. and {Nieselt-Struwe}, K. and Schuster, S.~C.},
year = {2005}, year = {2005},
title = {Whole-genome prokaryotic phylogeny}, title = {Whole-genome prokaryotic phylogeny},
journal = {Bioinformatics}, journal = {Bioinformatics},
...@@ -155,7 +155,7 @@ ...@@ -155,7 +155,7 @@
} }
@article{hoang2018a, @article{hoang2018a,
author = {Hoang, DT and Chernomor, O and von Haeseler, A and Minh, BQ and Vinh, LS}, author = {Hoang, D.~T. and Chernomor, O. and {von Haeseler}, A. and Minh, B.~Q. and Vinh, L.~S.},
year = {2018}, year = {2018},
title = {UFBoot2: improving the ultrafast bootstrap approximation}, title = {UFBoot2: improving the ultrafast bootstrap approximation},
journal = {Molecular Biology and Evolution}, journal = {Molecular Biology and Evolution},
...@@ -167,7 +167,7 @@ ...@@ -167,7 +167,7 @@
} }
@article{hoang2018b, @article{hoang2018b,
author = {Hoang, DY and Vinh, LS and Flouri, T and Stamatakis, A and von Haeseler, A and Minh, BQ}, author = {Hoang, D.~T. and Vinh, L.~S. and Flouri, T. and Stamatakis, A. and {von Haeseler}, A. and Minh, B.~Q.},
year = {2018}, year = {2018},
title = {MPBoot: fast phylogenetic maximum parsimony tree inference and bootstrap approximation}, title = {MPBoot: fast phylogenetic maximum parsimony tree inference and bootstrap approximation},
journal = {BMC Evolutionary Biology}, journal = {BMC Evolutionary Biology},
...@@ -179,7 +179,7 @@ ...@@ -179,7 +179,7 @@
} }
@article{house2014, @article{house2014,
author = {House, CH and Pellegrini, M and Fitz-Gibbon, ST}, author = {House, C.~H. and Pellegrini, M. and {Fitz-Gibbon}, S.~T.},
year = {2014}, year = {2014},
title = {Genome-wide gene order distances support clustering the gram-positive bacteria}, title = {Genome-wide gene order distances support clustering the gram-positive bacteria},
journal = {Frontiers in Microbiology}, journal = {Frontiers in Microbiology},
...@@ -190,7 +190,7 @@ ...@@ -190,7 +190,7 @@
} }
@article{krajewski1990, @article{krajewski1990,
author = {Krajewski, C and Dickerman, AW}, author = {Krajewski, C. and Dickerman, A.~W.},
year = {1990}, year = {1990},
title = {Bootstrap analysis of phylogenetic trees derived from DNA hydridization distances}, title = {Bootstrap analysis of phylogenetic trees derived from DNA hydridization distances},
journal = {Systematic Zoology}, journal = {Systematic Zoology},
...@@ -202,7 +202,7 @@ ...@@ -202,7 +202,7 @@
} }
@article{lemoine2018, @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}, year = {2018},
title = {Renewing Felsenstein's phylogenetic bootstrap in the era of big data}, title = {Renewing Felsenstein's phylogenetic bootstrap in the era of big data},
journal = {Nature}, journal = {Nature},
...@@ -214,7 +214,7 @@ ...@@ -214,7 +214,7 @@
} }
@article{makarenkov2010, @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}, year = {2010},
title = {Weighted bootstrapping: a correction method for assessing the robustness of phylogenetic trees}, title = {Weighted bootstrapping: a correction method for assessing the robustness of phylogenetic trees},
journal = {BMC Evolutionary Biology}, journal = {BMC Evolutionary Biology},
...@@ -225,7 +225,7 @@ ...@@ -225,7 +225,7 @@
} }
@article{minh2013, @article{minh2013,
author = {Minh, BQ and Nguyen, MA and von Haeseler, A}, author = {Minh, B.~Q. and Nguyen, M.~A. and {von Haeseler}, A.},
year = {2013}, year = {2013},
title = {Ultrafast approximation for phylogenetic bootstrap}, title = {Ultrafast approximation for phylogenetic bootstrap},
journal = {Molecular Biology and Evolution}, journal = {Molecular Biology and Evolution},
...@@ -237,18 +237,18 @@ ...@@ -237,18 +237,18 @@
} }
@incollection{pardi2016, @incollection{pardi2016,
author = {Pardi, F and Gascuel, O}, author = {Pardi, F. and Gascuel, O.},
year = {2016}, year = {2016},
title = {Distance-based methods in phylogenetics}, title = {Distance-based methods in phylogenetics},
booktitle = {Encyclopedia of Evolutionary Biology}, booktitle = {Encyclopedia of Evolutionary Biology},
editor = {Kliman R}, editor = {Kliman, R.},
publisher = {Academic Press}, publisher = {Academic Press},
pages = {458--465}, pages = {458--465},
url = {https://hal-lirmm.ccsd.cnrs.fr/lirmm-01386569} url = {https://hal-lirmm.ccsd.cnrs.fr/lirmm-01386569}
} }
@article{saitou1987, @article{saitou1987,
author = {Saitou, N and Nei, M}, author = {Saitou, N. and Nei, M.},
year = {1987}, year = {1987},
title = {The neighbor-joining method: a new method for reconstructing phylogenetic trees}, title = {The neighbor-joining method: a new method for reconstructing phylogenetic trees},
journal = {Molecular Biology and Evolution}, journal = {Molecular Biology and Evolution},
...@@ -260,7 +260,7 @@ ...@@ -260,7 +260,7 @@
} }
@article{spencer2007, @article{spencer2007,
author = {Spencer, M and Bryant, D and Susko, E}, author = {Spencer, M. and Bryant, D. and Susko, E.},
year = {2007}, year = {2007},
title = {Conditioned genome reconstruction: how to avoid choosing the conditioning genome}, title = {Conditioned genome reconstruction: how to avoid choosing the conditioning genome},
journal = {Systematic Biology}, journal = {Systematic Biology},
...@@ -272,7 +272,7 @@ ...@@ -272,7 +272,7 @@
} }
@article{studier1988, @article{studier1988,
author = {Studier, JA and Kepler, KJ}, author = {Studier, J.~A. and Kepler, K.~J.},
year = {1988}, year = {1988},
title = {A note on the neighbour-joining method of Saitou and Nei}, title = {A note on the neighbour-joining method of Saitou and Nei},
journal = {Molecular Biology and Evolution}, journal = {Molecular Biology and Evolution},
...@@ -284,7 +284,7 @@ ...@@ -284,7 +284,7 @@
} }
@article{wang2006, @article{wang2006,
author = {Wang, LS and Warnow, T and Moret, BM and Jansen, RK and Raubeson, LA}, author = {Wang, L.~S. and Warnow, T. and Moret, B.~M. and Jansen, R.~K. and Raubeson, L.~A.},
year = {2006}, year = {2006},
title = {Distance-based genome rearrangement phylogeny}, title = {Distance-based genome rearrangement phylogeny},
journal = {Journal of Molecular Evolution}, journal = {Journal of Molecular Evolution},
...@@ -296,7 +296,7 @@ ...@@ -296,7 +296,7 @@
} }
@article{zaretskii1965, @article{zaretskii1965,
author = {Zaretskii, ZA}, author = {Zaretskii, Z.~A.},
year = {1965}, year = {1965},
title = {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]}, note = {ПОСТРОЕНИЕ ДЕРЕВА ПО НАБОРУ РАССТОЯНИЙ МЕЖДУ ВИСЯЧИМИ ВЕРШИНАМИ [real title]},
......
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