diff --git a/paper/paper.bib b/paper/paper.bib
index ee5d569f90f1cb3e996f933c9bd1849d2f614a0f..85d3b0dd7967ab61ad17504ad0ac259519d8ab8c 100644
--- a/paper/paper.bib
+++ b/paper/paper.bib
@@ -1,5 +1,5 @@
@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, F.~R. and Kendall, D.~G. 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, P.~J.},
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, 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},
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},
@@ -130,11 +130,11 @@
}
@inproceedings{guenoche2001,
- author = {Guénoche, A and Garreta, H},
+ 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},
+ editor = {Gascuel, O. and Sagot, M.-F.},
pages = {45--56},
publisher = {Springer Berlin Heidelberg},
address = {Berlin, Heidelberg},
@@ -143,7 +143,7 @@
}
@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},
title = {Whole-genome prokaryotic phylogeny},
journal = {Bioinformatics},
@@ -155,7 +155,7 @@
}
@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},
title = {UFBoot2: improving the ultrafast bootstrap approximation},
journal = {Molecular Biology and Evolution},
@@ -167,7 +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, D.~T. and Vinh, L.~S. and Flouri, T. and Stamatakis, A. and {von Haeseler}, A. and Minh, B.~Q.},
year = {2018},
title = {MPBoot: fast phylogenetic maximum parsimony tree inference and bootstrap approximation},
journal = {BMC Evolutionary Biology},
@@ -179,7 +179,7 @@
}
@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},
title = {Genome-wide gene order distances support clustering the gram-positive bacteria},
journal = {Frontiers in Microbiology},
@@ -190,7 +190,7 @@
}
@article{krajewski1990,
- author = {Krajewski, C and Dickerman, AW},
+ author = {Krajewski, C. and Dickerman, A.~W.},
year = {1990},
title = {Bootstrap analysis of phylogenetic trees derived from DNA hydridization distances},
journal = {Systematic Zoology},
@@ -202,7 +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},
@@ -214,7 +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},
@@ -225,7 +225,7 @@
}
@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},
title = {Ultrafast approximation for phylogenetic bootstrap},
journal = {Molecular Biology and Evolution},
@@ -237,18 +237,18 @@
}
@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},
- editor = {Kliman R},
+ editor = {Kliman, R.},
publisher = {Academic Press},
pages = {458--465},
url = {https://hal-lirmm.ccsd.cnrs.fr/lirmm-01386569}
}
@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},
@@ -260,7 +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},
@@ -272,7 +272,7 @@
}
@article{studier1988,
- author = {Studier, JA and Kepler, KJ},
+ author = {Studier, J.~A. and Kepler, K.~J.},
year = {1988},
title = {A note on the neighbour-joining method of Saitou and Nei},
journal = {Molecular Biology and Evolution},
@@ -284,7 +284,7 @@
}
@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},
title = {Distance-based genome rearrangement phylogeny},
journal = {Journal of Molecular Evolution},
@@ -296,7 +296,7 @@
}
@article{zaretskii1965,
- author = {Zaretskii, ZA},
+ author = {Zaretskii, Z.~A.},
year = {1965},
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]},