manuscript.bib

@article{smith2020phylogenetic,
  title={Phylogenetic conflicts, combinability, and deep phylogenomics in plants},
  author={Smith, Stephen A and Walker-Hale, Nathanael and Walker, Joseph F and Brown, Joseph W},
  journal={Systematic Biology},
  volume={69},
  number={3},
  pages={579--592},
  year={2020},
  publisher={Oxford University Press}
}

@article{yu2018two,
  title={Two methods for mapping and visualizing associated data on phylogeny using ggtree},
  author={Yu, Guangchuang and Lam, Tommy Tsan-Yuk and Zhu, Huachen and Guan, Yi},
  journal={Molecular biology and evolution},
  volume={35},
  number={12},
  pages={3041--3043},
  year={2018},
  publisher={Oxford University Press}
}

@article{graham2002rooting,
  title={Rooting phylogenetic trees with distant outgroups: a case study from the commelinoid monocots},
  author={Graham, Sean W and Olmstead, Richard G and Barrett, Spencer CH},
  journal={Molecular biology and evolution},
  volume={19},
  number={10},
  pages={1769--1781},
  year={2002},
  publisher={Oxford University Press}
}

@Article{Camacho:2009,
author={Camacho, Christiam
and Coulouris, George
and Avagyan, Vahram
and Ma, Ning
and Papadopoulos, Jason
and Bealer, Kevin
and Madden, Thomas L.},
title={BLAST+: architecture and applications},
journal={BMC Bioinformatics},
year={2009},
volume={10},
number={1},
pages={421},
abstract={Sequence similarity searching is a very important bioinformatics task. While Basic Local Alignment Search Tool (BLAST) outperforms exact methods through its use of heuristics, the speed of the current BLAST software is suboptimal for very long queries or database sequences. There are also some shortcomings in the user-interface of the current command-line applications.},
issn={1471-2105},
doi={10.1186/1471-2105-10-421},
url={https://doi.org/10.1186/1471-2105-10-421}
}

@article{Buchfink:2014,
author={Buchfink, Benjamin and Xie, Chao and Huson, Daniel H.},
title={Fast and sensitive protein alignment using DIAMOND},
journal={Nature Methods},
year={2014},
month={Nov},
day={17},
publisher={Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved. SN  -},
volume={12},
pages={59 EP  -},
url={https://doi.org/10.1038/nmeth.3176}
}

@article{nosenko2013deep,
  title={Deep metazoan phylogeny: when different genes tell different stories},
  author={Nosenko, Tetyana and Schreiber, Fabian and Adamska, Maja and Adamski, Marcin and Eitel, Michael and Hammel, J{\"o}rg and Maldonado, Manuel and M{\"u}ller, Werner EG and Nickel, Michael and Schierwater, Bernd and others},
  journal={Molecular phylogenetics and evolution},
  volume={67},
  number={1},
  pages={223--233},
  year={2013},
  publisher={Elsevier}
}

@article{kalyaanamoorthy2017modelfinder,
  title={ModelFinder: fast model selection for accurate phylogenetic estimates},
  author={Kalyaanamoorthy, Subha and Minh, Bui Quang and Wong, Thomas KF and von Haeseler, Arndt and Jermiin, Lars S},
  journal={Nature methods},
  volume={14},
  number={6},
  pages={587},
  year={2017},
  publisher={Nature Publishing Group}
}
@article{nguyen2014iq,
  title={IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies},
  author={Nguyen, Lam-Tung and Schmidt, Heiko A and von Haeseler, Arndt and Minh, Bui Quang},
  journal={Molecular biology and evolution},
  volume={32},
  number={1},
  pages={268--274},
  year={2014},
  publisher={Oxford University Press}
}
@article{Castresana:2000vy,
author = {Castresana, J.},
title = {{Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis}},
journal = {Molecular Biology and Evolution},
year = {2000},
volume = {17},
number = {4},
pages = {540--552},
month = apr,
annote = {0737-4038 (Print)
Journal Article},
affiliation = {European Molecular Biology Laboratory, Heidelberg, Germany. jose.castresana@embl-heidelberg.de},
pmid = {10742046},
rating = {0},
date-added = {2011-04-23T11:49:28GMT},
date-modified = {2015-04-08T17:40:49GMT},
abstract = {The use of some multiple-sequence alignments in phylogenetic analysis, particularly those that are not very well conserved, requires the elimination of poorly aligned positions and divergent regions, since they may not be homologous or may have been saturated by multiple substitutions. A computerized method that eliminates such positions and at the same time tries to minimize the loss of informative sites is presented here. The method is based on the selection of blocks of positions that fulfill a simple set of requirements with respect to the number of contiguous conserved positions, lack of gaps, and high conservation of flanking positions, making the final alignment more suitable for phylogenetic analysis. To illustrate the efficiency of this method, alignments of 10 mitochondrial proteins from several completely sequenced mitochondrial genomes belonging to diverse eukaryotes were used as examples. The percentages of removed positions were higher in the most divergent alignments. After removing divergent segments, the amino acid composition of the different sequences was more uniform, and pairwise distances became much smaller. Phylogenetic trees show that topologies can be different after removing conserved blocks, particularly when there are several poorly resolved nodes. Strong support was found for the grouping of animals and fungi but not for the position of more basal eukaryotes. The use of a computerized method such as the one presented here reduces to a certain extent the necessity of manually editing multiple alignments, makes the automation of phylogenetic analysis of large data sets feasible, and facilitates the reproduction of the final alignment by other researchers.},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10742046 },
uri = {\url{papers3://publication/uuid/C35BDD6F-8455-47FC-A38D-44C99C608AA5}}
}



@article{Dunn:2008ky,
author = {Dunn, Casey W and Hejnol, Andreas and Matus, David Q and Pang, Kevin and Browne, William E and Smith, Stephen A and Seaver, Elaine and Rouse, Greg W and Obst, Matthias and Edgecombe, Gregory D and S{\o}rensen, Martin V and Haddock, Steven H D and Schmidt-Rhaesa, Andreas and Okusu, Akiko and Kristensen, Reinhardt Mobjerg and Wheeler, Ward C and Martindale, Mark Q and Giribet, Gonzalo},
title = {{Broad phylogenomic sampling improves resolution of the animal tree of life}},
journal = {Nature},
year = {2008},
volume = {452},
number = {7188},
pages = {745--749},
month = mar,
doi = {10.1038/nature06614},
read = {Yes},
rating = {0},
date-added = {2014-11-10T23:49:19GMT},
date-modified = {2018-10-15T17:27:49GMT},
url = {http://www.nature.com/doifinder/10.1038/nature06614},
local-url = {file://localhost/Users/cdunn/Dropbox/articles/Library.papers3/Files/03/03D02062-0510-4195-A06D-D0A67E8DEDC0.pdf},
file = {{03D02062-0510-4195-A06D-D0A67E8DEDC0.pdf:/Users/cdunn/Dropbox/articles/Library.papers3/Files/03/03D02062-0510-4195-A06D-D0A67E8DEDC0.pdf:application/pdf;03D02062-0510-4195-A06D-D0A67E8DEDC0.pdf:/Users/cdunn/Dropbox/articles/Library.papers3/Files/03/03D02062-0510-4195-A06D-D0A67E8DEDC0.pdf:application/pdf}},
uri = {\url{papers3://publication/doi/10.1038/nature06614}}
}

@article{Enright:2002uq,
author = {Enright, AJ and Van Dongen, S. and Ouzounis, CA},
title = {{An efficient algorithm for large-scale detection of protein families}},
journal = {Nucleic Acids Research},
year = {2002},
volume = {30},
number = {7},
pages = {1575--1584},
publisher = {Oxford University Press},
affiliation = {European Bioinformat Inst, EMBL Cambridge Outstn, Computat Gen Grp, Cambridge CB10 1SD, England},
keywords = {molecular homology},
doi = {10.1093/nar/30.7.1575},
pmid = {11917018},
pmcid = {PMC101833},
language = {English},
read = {Yes},
rating = {0},
date-added = {2011-04-21T20:37:46GMT},
date-modified = {2015-04-08T17:39:59GMT},
abstract = {Detection of protein families in large databases is one of the principal research objectives in structural and functional genomics. Protein family classification can significantly contribute to the delineation of functional diversity of homologous proteins, the prediction of function based on domain architecture or the presence of sequence motifs as well as comparative genomics, providing valuable evolutionary insights. We present a novel approach called TRIBE-MCL for rapid and accurate clustering of protein sequences into families. The method relies on the Markov cluster (MCL) algorithm for the assignment of proteins into families based on precomputed sequence similarity information. This novel approach does not suffer from the problems that normally hinder other protein sequence clustering algorithms, such as the presence of multi-domain proteins, promiscuous domains and fragmented proteins. The method has been rigorously tested and validated on a number of very large databases, including SwissProt, InterPro, SCOP and the draft human genome. Our results indicate that the method is ideally suited to the rapid and accurate detection of protein families on a large scale. The method has been used to detect and categorise protein families within the draft human genome and the resulting families have been used to annotate a large proportion of human proteins.},
url = {http://nar.oxfordjournals.org/lookup/doi/10.1093/nar/30.7.1575},
local-url = {file://localhost/Users/cdunn/Dropbox/articles/Library.papers3/Articles/2002/Enright/Nucleic%20Acids%20Research%202002%20Enright.pdf},
file = {{Nucleic Acids Research 2002 Enright.pdf:/Users/cdunn/Dropbox/articles/Library.papers3/Articles/2002/Enright/Nucleic Acids Research 2002 Enright.pdf:application/pdf;Nucleic Acids Research 2002 Enright.pdf:/Users/cdunn/Dropbox/articles/Library.papers3/Articles/2002/Enright/Nucleic Acids Research 2002 Enright.pdf:application/pdf}},
uri = {\url{papers3://publication/doi/10.1093/nar/30.7.1575}}
}

@article{Felsenstein:1981vk,
author = {Felsenstein, J.},
title = {{Evolutionary trees from DNA sequences: a maximum likelihood approach.}},
journal = {Journal of Molecular Evolution},
year = {1981},
volume = {17},
number = {6},
pages = {368--376},
pmid = {7288891},
language = {English},
read = {Yes},
rating = {0},
date-added = {2018-10-16T15:34:12GMT},
date-modified = {2018-10-16T15:35:05GMT},
abstract = {The application of maximum likelihood techniques to the estimation of evolutionary trees from nucleic acid sequence data is discussed. A computationally feasible method for finding such maximum likelihood estimates is developed, and a computer program is available. This method has advantages over the traditional parsimony algorithms, which can give misleading results if rates of evolution differ in different lineages. It also allows the testing of hypotheses about the constancy of evolutionary rates by likelihood ratio tests, and gives rough indication of the error of ;the estimate of the tree.},
url = {http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&id=7288891&retmode=ref&cmd=prlinks},
local-url = {file://localhost/Users/cdunn/Dropbox/articles/Library.papers3/Files/D7/D7C6E6E8-AA6E-4D17-822C-E383AE558B4C.pdf},
file = {{D7C6E6E8-AA6E-4D17-822C-E383AE558B4C.pdf:/Users/cdunn/Dropbox/articles/Library.papers3/Files/D7/D7C6E6E8-AA6E-4D17-822C-E383AE558B4C.pdf:application/pdf}},
uri = {\url{papers3://publication/uuid/85009339-08F2-4648-81A3-A0827CE1E30C}}
}

@InProceedings{Hagberg:2008,
author = {Aric A. Hagberg and Daniel A. Schult and Pieter J. Swart},
title = {Exploring Network Structure, Dynamics, and Function using NetworkX},
booktitle = {Proceedings of the 7th Python in Science Conference},
pages = {11 - 15},
address = {Pasadena, CA USA},
year = {2008},
editor ={Ga\"el Varoquaux and Travis Vaught and Jarrod Millman}
}

@article{Lartillot:2004dq,
author = {Lartillot, N},
title = {{A Bayesian Mixture Model for Across-Site Heterogeneities in the Amino-Acid Replacement Process}},
journal = {Molecular Biology and Evolution},
year = {2004},
volume = {21},
number = {6},
pages = {1095--1109},
month = feb,
keywords = {MOLECULAR EVOLUTION, PHYLOGENETIC METHODS},
doi = {10.1093/molbev/msh112},
language = {English},
read = {Yes},
rating = {0},
date-added = {2011-04-21T20:44:20GMT},
date-modified = {2017-03-23T06:18:29GMT},
url = {http://mbe.oupjournals.org/cgi/doi/10.1093/molbev/msh112},
local-url = {file://localhost/Users/cdunn/Dropbox/articles/Library.papers3/Articles/2004/Lartillot/Molecular%20Biology%20and%20Evolution%202004%20Lartillot.pdf},
file = {{Molecular Biology and Evolution 2004 Lartillot.pdf:/Users/cdunn/Dropbox/articles/Library.papers3/Articles/2004/Lartillot/Molecular Biology and Evolution 2004 Lartillot.pdf:application/pdf;Molecular Biology and Evolution 2004 Lartillot.pdf:/Users/cdunn/Dropbox/articles/Library.papers3/Articles/2004/Lartillot/Molecular Biology and Evolution 2004 Lartillot.pdf:application/pdf}},
uri = {\url{papers3://publication/doi/10.1093/molbev/msh112}}
}

@article{Le:2008fp,
author = {Le, Si Quang and Gascuel, Olivier},
title = {{An improved general amino acid replacement matrix.}},
journal = {Molecular Biology and Evolution},
year = {2008},
volume = {25},
number = {7},
pages = {1307--1320},
month = jul,
affiliation = {M{\'e}thodes et Algorithmes pour la Bioinformatique, LIRMM, CNRS, Universit{\'e} Montpellier II, Montpellier, France.},
doi = {10.1093/molbev/msn067},
pmid = {18367465},
language = {English},
read = {Yes},
rating = {0},
date-added = {2018-10-16T16:16:35GMT},
date-modified = {2018-10-16T16:38:09GMT},
abstract = {Amino acid replacement matrices are an essential basis of protein phylogenetics. They are used to compute substitution probabilities along phylogeny branches and thus the likelihood of the data. They are also essential in protein alignment. A number of replacement matrices and methods to estimate these matrices from protein alignments have been proposed since the seminal work of Dayhoff et al. (1972). An important advance was achieved by Whelan and Goldman (2001) and their WAG matrix, thanks to an efficient maximum likelihood estimation approach that accounts for the phylogenies of sequences within each training alignment. We further refine this method by incorporating the variability of evolutionary rates across sites in the matrix estimation and using a much larger and diverse database than BRKALN, which was used to estimate WAG. To estimate our new matrix (called LG after the authors), we use an adaptation of the XRATE software and 3,912 alignments from Pfam, comprising approximately 50,000 sequences and approximately 6.5 million residues overall. To evaluate the LG performance, we use an independent sample consisting of 59 alignments from TreeBase and randomly divide Pfam alignments into 3,412 training and 500 test alignments. The comparison with WAG and JTT shows a clear likelihood improvement. With TreeBase, we find that 1) the average Akaike information criterion gain per site is 0.25 and 0.42, when compared with WAG and JTT, respectively; 2) LG is significantly better than WAG for 38 alignments (among 59), and significantly worse with 2 alignments only; and 3) tree topologies inferred with LG, WAG, and JTT frequently differ, indicating that using LG impacts not only the likelihood value but also the output tree. Results with the test alignments from Pfam are analogous. LG and a PHYML implementation can be downloaded from http://atgc.lirmm.fr/LG.},
url = {https://academic.oup.com/mbe/article-lookup/doi/10.1093/molbev/msn067},
local-url = {file://localhost/Users/cdunn/Dropbox/articles/Library.papers3/Files/73/733401AF-0CA2-429F-9B67-FA026C33633A.pdf},
file = {{733401AF-0CA2-429F-9B67-FA026C33633A.pdf:/Users/cdunn/Dropbox/articles/Library.papers3/Files/73/733401AF-0CA2-429F-9B67-FA026C33633A.pdf:application/pdf}},
uri = {\url{papers3://publication/doi/10.1093/molbev/msn067}}
}

@article{laumer2019revisiting,
  title={Revisiting metazoan phylogeny with genomic sampling of all phyla},
  author={Laumer, Christopher E and Fern{\'a}ndez, Rosa and Lemer, Sarah and Combosch, David and Kocot, Kevin M and Riesgo, Ana and Andrade, S{\'o}nia CS and Sterrer, Wolfgang and S{\o}rensen, Martin V and Giribet, Gonzalo},
  journal={Proceedings of the royal society B},
  volume={286},
  number={1906},
  pages={20190831},
  year={2019},
  publisher={The Royal Society}
}


@article{Philippe:2009hh,
author = {Philippe, HervE and Derelle, Romain and Lopez, Philippe and Pick, Kerstin and Borchiellini, Carole and Boury-Esnault, Nicole and Vacelet, Jean and Renard, Emmanuelle and Houliston, Evelyn and QuEinnec, Eric and Da Silva, Corinne and Wincker, Patrick and Le Guyader, HervE and Leys, Sally and Jackson, Daniel J and Schreiber, Fabian and Erpenbeck, Dirk and Morgenstern, Burkhard and WOrheide, Gert and Manuel, MichaEl},
title = {{Phylogenomics revives traditional views on deep animal relationships}},
journal = {Current biology : CB},
year = {2009},
volume = {19},
number = {8},
pages = {706--712},
month = apr,
publisher = {Elsevier Ltd},
keywords = {Phylogeny},
doi = {10.1016/j.cub.2009.02.052},
read = {Yes},
rating = {0},
date-added = {2011-04-21T20:37:47GMT},
date-modified = {2018-07-26T03:27:58GMT},
url = {http://dx.doi.org/10.1016/j.cub.2009.02.052},
local-url = {file://localhost/Users/cdunn/Dropbox/articles/Library.papers3/Articles/2009/Philippe/Curr.%20Biol.%202009%20Philippe.pdf},
file = {{Curr. Biol. 2009 Philippe.pdf:/Users/cdunn/Dropbox/articles/Library.papers3/Articles/2009/Philippe/Curr. Biol. 2009 Philippe.pdf:application/pdf;Curr. Biol. 2009 Philippe.pdf:/Users/cdunn/Dropbox/articles/Library.papers3/Articles/2009/Philippe/Curr. Biol. 2009 Philippe.pdf:application/pdf}},
uri = {\url{papers3://publication/doi/10.1016/j.cub.2009.02.052}}
}




@article{Pick:2010eb,
author = {Pick, K S and Philippe, H and Schreiber, F and Erpenbeck, D and Jackson, D J and Wrede, P and Wiens, M and Alie, A and Morgenstern, B and Manuel, M and Worheide, G},
title = {{Improved phylogenomic taxon sampling noticeably affects nonbilaterian relationships}},
journal = {Molecular Biology and Evolution},
year = {2010},
volume = {27},
number = {9},
month = aug,
keywords = {Phylogeny},
doi = {10.1093/molbev/msq089},
language = {English},
read = {Yes},
rating = {0},
date-added = {2011-04-21T21:07:08GMT},
date-modified = {2018-08-20T22:39:57GMT},
url = {http://mbe.oxfordjournals.org/cgi/doi/10.1093/molbev/msq089},
local-url = {file://localhost/Users/cdunn/Dropbox/articles/Library.papers3/Articles/2010/Pick/Molecular%20Biology%20and%20Evolution%202010%20Pick.pdf},
file = {{Molecular Biology and Evolution 2010 Pick.pdf:/Users/cdunn/Dropbox/articles/Library.papers3/Articles/2010/Pick/Molecular Biology and Evolution 2010 Pick.pdf:application/pdf;Molecular Biology and Evolution 2010 Pick.pdf:/Users/cdunn/Dropbox/articles/Library.papers3/Articles/2010/Pick/Molecular Biology and Evolution 2010 Pick.pdf:application/pdf}},
uri = {\url{papers3://publication/doi/10.1093/molbev/msq089}}
}

@article{Ronquist:2003hx,
author = {Ronquist, F and Huelsenbeck, J P},
title = {{MrBayes 3: Bayesian phylogenetic inference under mixed models}},
journal = {Bioinformatics},
year = {2003},
volume = {19},
number = {12},
pages = {1572--1574},
month = aug,
keywords = {PHYLOGENETIC METHODS},
doi = {10.1093/bioinformatics/btg180},
language = {English},
rating = {0},
date-added = {2011-04-21T20:45:36GMT},
date-modified = {2016-03-22T14:44:46GMT},
url = {http://www.bioinformatics.oupjournals.org/cgi/doi/10.1093/bioinformatics/btg180},
local-url = {file://localhost/Users/cdunn/Dropbox/articles/Library.papers3/Articles/2003/Ronquist/Bioinformatics%20(Oxford%20England)%202003%20Ronquist.pdf},
file = {{Bioinformatics (Oxford England) 2003 Ronquist.pdf:/Users/cdunn/Dropbox/articles/Library.papers3/Articles/2003/Ronquist/Bioinformatics (Oxford England) 2003 Ronquist.pdf:application/pdf}},
uri = {\url{papers3://publication/doi/10.1093/bioinformatics/btg180}}
}



@article{Smith:2008gb,
author = {Smith, Stephen A and Dunn, Casey W},
title = {{Phyutility: a phyloinformatics tool for trees, alignments and molecular data.}},
journal = {Bioinformatics},
year = {2008},
volume = {24},
number = {5},
pages = {715--716},
month = mar,
publisher = {Oxford University Press},
affiliation = {Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA. stephen.smith@yale.edu},
doi = {10.1093/bioinformatics/btm619},
pmid = {18227120},
language = {English},
rating = {0},
date-added = {2016-12-30T19:31:26GMT},
date-modified = {2018-10-16T13:14:09GMT},
abstract = {SUMMARY:Phyutility provides a set of phyloinformatics tools for summarizing and manipulating phylogenetic trees, manipulating molecular data and retrieving data from NCBI. Its simple command-line interface allows for easy integration into scripted analyses, and is able to handle large datasets with an integrated database.

AVAILABILITY:Phyutility, including source code, documentation, examples, and executables, is available at http://code.google.com/p/phyutility.},
url = {https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btm619},
local-url = {file://localhost/Users/cdunn/Dropbox/articles/Library.papers3/Files/64/643AD35C-79A6-49E7-AEA2-6A7BC14AA759.pdf},
file = {{643AD35C-79A6-49E7-AEA2-6A7BC14AA759.pdf:/Users/cdunn/Dropbox/articles/Library.papers3/Files/64/643AD35C-79A6-49E7-AEA2-6A7BC14AA759.pdf:application/pdf}},
uri = {\url{papers3://publication/doi/10.1093/bioinformatics/btm619}}
}

@article{Stamatakis:2006wc,
author = {Stamatakis, Alexandros},
title = {{RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models.}},
journal = {Bioinformatics},
year = {2006},
volume = {22},
number = {21},
pages = {2688--2690},
month = nov,
annote = {1460-2059 (Electronic)
Evaluation Studies
Journal Article
Research Support, Non-U.S. Gov't},
affiliation = {Swiss Federal Institute of Technology Lausanne, School of Computer and Communication Sciences Lab Prof. Moret, STATION 14, CH-1015 Lausanne, Switzerland. Alexandros.Stamatakis@epfl.ch},
keywords = {bioinformatics, PHYLOGENETIC METHODS},
doi = {10.1093/bioinformatics/btl446},
pmid = {16928733},
language = {English},
rating = {0},
date-added = {2011-04-23T11:50:00GMT},
date-modified = {2016-03-22T15:47:48GMT},
abstract = {UNLABELLED:RAxML-VI-HPC (randomized axelerated maximum likelihood for high performance computing) is a sequential and parallel program for inference of large phylogenies with maximum likelihood (ML). Low-level technical optimizations, a modification of the search algorithm, and the use of the GTR+CAT approximation as replacement for GTR+Gamma yield a program that is between 2.7 and 52 times faster than the previous version of RAxML. A large-scale performance comparison with GARLI, PHYML, IQPNNI and MrBayes on real data containing 1000 up to 6722 taxa shows that RAxML requires at least 5.6 times less main memory and yields better trees in similar times than the best competing program (GARLI) on datasets up to 2500 taxa. On datasets > or =4000 taxa it also runs 2-3 times faster than GARLI. RAxML has been parallelized with MPI to conduct parallel multiple bootstraps and inferences on distinct starting trees. The program has been used to compute ML trees on two of the largest alignments to date containing 25,057 (1463 bp) and 2182 (51,089 bp) taxa, respectively.

AVAILABILITY:icwww.epfl.ch/{\textasciitilde}stamatak},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16928733 },
local-url = {file://localhost/Users/cdunn/Dropbox/articles/Library.papers3/Articles/2006/Stamatakis/Bioinformatics%20(Oxford%20England)%202006%20Stamatakis.pdf},
file = {{Bioinformatics (Oxford England) 2006 Stamatakis.pdf:/Users/cdunn/Dropbox/articles/Library.papers3/Articles/2006/Stamatakis/Bioinformatics (Oxford England) 2006 Stamatakis.pdf:application/pdf;Bioinformatics (Oxford England) 2006 Stamatakis.pdf:/Users/cdunn/Dropbox/articles/Library.papers3/Articles/2006/Stamatakis/Bioinformatics (Oxford England) 2006 Stamatakis.pdf:application/pdf}},
uri = {\url{papers3://publication/doi/10.1093/bioinformatics/btl446}}
}

@article{podar2001,
  title={A molecular phylogenetic framework for the phylum Ctenophora using 18S rRNA genes},
  author={Podar, Mircea and Haddock, Steven HD and Sogin, Mitchell L and Harbison, G Richard},
  journal={Molecular phylogenetics and evolution},
  volume={21},
  number={2},
  pages={218--230},
  year={2001},
  publisher={Elsevier}
}


@article{Thorley:1999kg,
author = {Thorley, JL and Wilkinson, M.},
title = {{Testing the phylogenetic stability of early tetrapods}},
journal = {Journal of Theoretical Biology},
year = {1999},
volume = {200},
number = {3},
pages = {343--344},
month = oct,
affiliation = {School of Biological Sciences, University of Bristol, Bristol, BS8 1UG, U.K.},
keywords = {PHYLOGENETIC METHODS},
doi = {10.1006/jtbi.1999.0999},
pmid = {10527723},
language = {English},
rating = {0},
date-added = {2011-04-21T20:44:24GMT},
date-modified = {2015-07-24T14:01:33GMT},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0022519399909992},
local-url = {file://localhost/Users/cdunn/Dropbox/articles/Library.papers3/Articles/1999/Thorley/Journal%20of%20Theoretical%20Biology%201999%20Thorley.pdf},
file = {{Journal of Theoretical Biology 1999 Thorley.pdf:/Users/cdunn/Dropbox/articles/Library.papers3/Articles/1999/Thorley/Journal of Theoretical Biology 1999 Thorley.pdf:application/pdf}},
uri = {\url{papers3://publication/doi/10.1006/jtbi.1999.0999}}
}



@article{Wallberg:2004ws,
author = {Wallberg, A and Thollesson, M and Farris, JS and Jondelius, U},
title = {{The phylogenetic position of the comb jellies (Ctenophora) and the importance of taxonomic sampling}},
journal = {Cladistics},
year = {2004},
volume = {20},
number = {6},
pages = {558--578},
affiliation = {Uppsala Univ, Evolutionary Biol Ctr, Dept Systemat Zool, SE-75236 Uppsala, Sweden},
keywords = {Phylogeny},
language = {English},
read = {Yes},
rating = {0},
date-added = {2011-04-21T20:42:19GMT},
date-modified = {2016-10-03T14:03:17GMT},
abstract = {The transition to a vermiform body shape is one of the most important events in animal evolution, having led to the impressive radiation of Bilateria. However, the sister group of Bilateria has remained obscure. Cladistic analyses of morphology indicate that Ctenophora is the sister group of Bilateria. Previous analyses of SSU rRNA sequences have yielded conflicting results; in many studies Ctenophora forms the sister group of Cnidaria + Bilateria. but in others the ctenophores group with poriferans. Here we re-examine the SSU sequence by analyzing a dataset with 528 metazoan + outgroup sequences, including almost 120 poriferan and diploblast sequences. We use parsimony ratchet and jackknife methods, as well as Bayesian methods, to analyze the data. The results indicate strong phylogenetic signals for a cnidarian + bilaterian group and for the comb jellies to have branched off early within a group uniting all epithelial animals [(Ct,(Cn,Bi))]. We demonstrate the importance of inclusive taxonomic coverage of ribosomal sequences for resolving this problematic part of the metazoan tree: topological stability increases dramatically with the addition of taxa, and the jackknife frequencies of the internal nodes uniting the lineages [(Cn,Bi) and ((Ct,(Cn,Bi))] also increase. We consider the reconstructed topology to represent the current best hypothesis of the interrelationships of these old lineages. Some morphological features supporting alternative hypotheses are discussed in the light of this result. (c) The Willi Hennig Society 2004.},
url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1096-0031.2004.00041.x/full},
local-url = {file://localhost/Users/cdunn/Dropbox/articles/Library.papers3/Articles/2004/Wallberg/Cladistics%202004%20Wallberg.pdf},
file = {{Cladistics 2004 Wallberg.pdf:/Users/cdunn/Dropbox/articles/Library.papers3/Articles/2004/Wallberg/Cladistics 2004 Wallberg.pdf:application/pdf}},
uri = {\url{papers3://publication/uuid/8D320503-343B-4010-8FD3-8B036CC3F1C7}}
}

@article{Whelan:2001ds,
author = {Whelan, Simon and Goldman, Nick},
title = {{A General Empirical Model of Protein Evolution Derived from Multiple Protein Families Using a Maximum-Likelihood Approach}},
journal = {Molecular Biology and Evolution},
year = {2001},
volume = {18},
number = {5},
pages = {691--699},
month = may,
doi = {10.1093/oxfordjournals.molbev.a003851},
language = {English},
read = {Yes},
rating = {0},
date-added = {2018-10-16T16:31:48GMT},
date-modified = {2018-10-16T16:33:51GMT},
url = {https://academic.oup.com/mbe/article-lookup/doi/10.1093/oxfordjournals.molbev.a003851},
local-url = {file://localhost/Users/cdunn/Dropbox/articles/Library.papers3/Files/B1/B17E8D94-74D3-4FDE-A7D7-F4E903FC4BE8.pdf},
file = {{B17E8D94-74D3-4FDE-A7D7-F4E903FC4BE8.pdf:/Users/cdunn/Dropbox/articles/Library.papers3/Files/B1/B17E8D94-74D3-4FDE-A7D7-F4E903FC4BE8.pdf:application/pdf}},
uri = {\url{papers3://publication/doi/10.1093/oxfordjournals.molbev.a003851}}
}

@article{salichos2013inferring,
  title={Inferring ancient divergences requires genes with strong phylogenetic signals},
  author={Salichos, Leonidas and Rokas, Antonis},
  journal={Nature},
  volume={497},
  number={7449},
  pages={327},
  year={2013},
  publisher={Nature Publishing Group}
}

@article{lanier2012recombination,
  title={Is recombination a problem for species-tree analyses?},
  author={Lanier, Hayley C and Knowles, L Lacey},
  journal={Systematic Biology},
  volume={61},
  number={4},
  pages={691--701},
  year={2012},
  publisher={Oxford University Press}
}

@article{hernandez2019six,
  title={Six-state amino acid recoding is not an effective strategy to offset the effects of compositional heterogeneity and saturation in phylogenetic analyses},
  author={Hernandez, Alexandra M and Ryan, Joseph F},
  journal={BioRxiv},
  pages={729103},
  year={2019},
  publisher={Cold Spring Harbor Laboratory}
}

@article{feuda2017improved,
  title={Improved modeling of compositional heterogeneity supports sponges as sister to all other animals},
  author={Feuda, Roberto and Dohrmann, Martin and Pett, Walker and Philippe, Herv{\'e} and Rota-Stabelli, Omar and Lartillot, Nicolas and W{\"o}rheide, Gert and Pisani, Davide},
  journal={Current Biology},
  volume={27},
  number={24},
  pages={3864--3870},
  year={2017},
  publisher={Elsevier}
}

@article{whelan2015error,
  title={Error, signal, and the placement of Ctenophora sister to all other animals},
  author={Whelan, Nathan V and Kocot, Kevin M and Moroz, Leonid L and Halanych, Kenneth M},
  journal={Proceedings of the National Academy of Sciences},
  volume={112},
  number={18},
  pages={5773--5778},
  year={2015},
  publisher={National Acad Sciences}
}

@article{chang2015genomic,
  title={Genomic insights into the evolutionary origin of Myxozoa within Cnidaria},
  author={Chang, E Sally and Neuhof, Moran and Rubinstein, Nimrod D and Diamant, Arik and Philippe, Herv{\'e} and Huchon, Doroth{\'e}e and Cartwright, Paulyn},
  journal={Proceedings of the National Academy of Sciences},
  volume={112},
  number={48},
  pages={14912--14917},
  year={2015},
  publisher={National Acad Sciences}
}

@article{hejnol2009assessing,
  title={Assessing the root of bilaterian animals with scalable phylogenomic methods},
  author={Hejnol, Andreas and Obst, Matthias and Stamatakis, Alexandros and Ott, Michael and Rouse, Greg W and Edgecombe, Gregory D and Martinez, Pedro and Bagu{\~n}{\`a}, Jaume and Bailly, Xavier and Jondelius, Ulf and others},
  journal={Proceedings of the Royal Society B: Biological Sciences},
  volume={276},
  number={1677},
  pages={4261--4270},
  year={2009},
  publisher={The Royal Society}
}

@article{borowiec2015extracting,
  title={Extracting phylogenetic signal and accounting for bias in whole-genome data sets supports the Ctenophora as sister to remaining Metazoa},
  author={Borowiec, Marek L and Lee, Ernest K and Chiu, Joanna C and Plachetzki, David C},
  journal={BMC genomics},
  volume={16},
  number={1},
  pages={987},
  year={2015},
  publisher={BioMed Central}
}

@article{whelan2017ctenophore,
  title={Ctenophore relationships and their placement as the sister group to all other animals},
  author={Whelan, Nathan V and Kocot, Kevin M and Moroz, Tatiana P and Mukherjee, Krishanu and Williams, Peter and Paulay, Gustav and Moroz, Leonid L and Halanych, Kenneth M},
  journal={Nature ecology \& evolution},
  volume={1},
  number={11},
  pages={1737},
  year={2017},
  publisher={Nature Publishing Group}
}

@article{simion2017large,
  title={A large and consistent phylogenomic dataset supports sponges as the sister group to all other animals},
  author={Simion, Paul and Philippe, Herve and Baurain, Denis and Jager, Muriel and Richter, Daniel J and Di Franco, Arnaud and Roure, Beatrice and Satoh, Nori and Queinnec, Eric and Ereskovsky, Alexander and others},
  journal={Current Biology},
  volume={27},
  number={7},
  pages={958--967},
  year={2017},
  publisher={Elsevier}
}
@article{whelan2016let,
  title={Who let the CAT out of the bag? Accurately dealing with substitutional heterogeneity in phylogenomic analyses},
  author={Whelan, Nathan V and Halanych, Kenneth M},
  journal={Systematic biology},
  volume={66},
  number={2},
  pages={232--255},
  year={2016},
  publisher={Oxford University Press}
}

@article{shen2017contentious,
    title={Contentious relationships in phylogenomic studies can be driven by a handful of genes},
    author={Shen, Xing-Xing and Hittinger, Chris Todd and Rokas, Antonis},
    journal={Nature Ecology \& Evolution},
    volume={1},
    number={5},
    pages={0126},
    year={2017},
    publisher={Nature Publishing Group}
  }

  @article{pisani2015genomic,
  title={Genomic data do not support comb jellies as the sister group to all other animals},
  author={Pisani, Davide and Pett, Walker and Dohrmann, Martin and Feuda, Roberto and Rota-Stabelli, Omar and Philippe, Herv{\'e} and Lartillot, Nicolas and W{\"o}rheide, Gert},
  journal={Proceedings of the National Academy of Sciences},
  volume={112},
  number={50},
  pages={15402--15407},
  year={2015},
  publisher={National Acad Sciences}
}
@article{philippe2011resolving,
  title={Resolving difficult phylogenetic questions: why more sequences are not enough},
  author={Philippe, Herv{\'e} and Brinkmann, Henner and Lavrov, Dennis V and Littlewood, D Timothy J and Manuel, Michael and W{\"o}rheide, Gert and Baurain, Denis},
  journal={PLoS biology},
  volume={9},
  number={3},
  pages={e1000602},
  year={2011},
  publisher={Public Library of Science}
}

@article{waterhouse2017busco,
  title={BUSCO applications from quality assessments to gene prediction and phylogenomics},
  author={Waterhouse, Robert M and Seppey, Mathieu and Sim{\~a}o, Felipe A and Manni, Mos{\`e} and Ioannidis, Panagiotis and Klioutchnikov, Guennadi and Kriventseva, Evgenia V and Zdobnov, Evgeny M},
  journal={Molecular biology and evolution},
  volume={35},
  number={3},
  pages={543--548},
  year={2017},
  publisher={Oxford University Press}
}
@article{shen2018tempo,
  title={Tempo and mode of genome evolution in the budding yeast subphylum},
  author={Shen, Xing-Xing and Opulente, Dana A and Kominek, Jacek and Zhou, Xiaofan and Steenwyk, Jacob L and Buh, Kelly V and Haase, Max AB and Wisecaver, Jennifer H and Wang, Mingshuang and Doering, Drew T and others},
  journal={Cell},
  volume={175},
  number={6},
  pages={1533--1545},
  year={2018},
  publisher={Elsevier}
}

@article{fernandez2018phylogenomics,
  title={Phylogenomics, diversification dynamics, and comparative transcriptomics across the spider tree of life},
  author={Fern{\'a}ndez, Rosa and Kallal, Robert J and Dimitrov, Dimitar and Ballesteros, Jes{\'u}s A and Arnedo, Miquel A and Giribet, Gonzalo and Hormiga, Gustavo},
  journal={Current Biology},
  volume={28},
  number={9},
  pages={1489--1497},
  year={2018},
  publisher={Elsevier}
}

@article{Blanquart:2008gl,
author = {Blanquart, S and Lartillot, N},
title = {{A Site- and Time-Heterogeneous Model of Amino Acid Replacement}},
journal = {Molecular Biology and Evolution},
year = {2008},
volume = {25},
number = {5},
pages = {842--858},
month = feb,
keywords = {PHYLOGENETIC METHODS},
doi = {10.1093/molbev/msn018},
language = {English},
read = {Yes},
rating = {0},
date-added = {2011-05-26T18:17:26GMT},
date-modified = {2017-09-28T14:14:01GMT},
url = {https://doi.org/10.1093/molbev/msn018},
local-url = {file://localhost/Users/cdunn/Dropbox/articles/Library.papers3/Articles/2008/Blanquart/Molecular%20Biology%20and%20Evolution%202008%20Blanquart.pdf},
file = {{Molecular Biology and Evolution 2008 Blanquart.pdf:/Users/cdunn/Dropbox/articles/Library.papers3/Articles/2008/Blanquart/Molecular Biology and Evolution 2008 Blanquart.pdf:application/pdf}},
uri = {\url{papers3://publication/doi/10.1093/molbev/msn018}}
}



@article{Bollback:2002to,
author = {Bollback, Jonathan P},
title = {{Bayesian model adequacy and choice in phylogenetics}},
journal = {Molecular Biology and Evolution},
year = {2002},
volume = {19},
number = {7},
pages = {1171--1180},
month = jul,
affiliation = {Department of Biology, University of Rochester, NY 14627, USA. bollback@brahms.biology.rochester.edu},
keywords = {PHYLOGENETIC METHODS},
pmid = {12082136},
language = {English},
read = {Yes},
rating = {0},
date-added = {2011-04-21T20:42:38GMT},
date-modified = {2018-04-10T16:13:33GMT},
abstract = {Bayesian inference is becoming a common statistical approach to phylogenetic estimation because, among other reasons, it allows for rapid analysis of large data sets with complex evolutionary models. Conveniently, Bayesian phylogenetic methods use currently available stochastic models of sequence evolution. However, as with other model-based approaches, the results of Bayesian inference are conditional on the assumed model of evolution: inadequate models (models that poorly fit the data) may result in erroneous inferences. In this article, I present a Bayesian phylogenetic method that evaluates the adequacy of evolutionary models using posterior predictive distributions. By evaluating a model's posterior predictive performance, an adequate model can be selected for a Bayesian phylogenetic study. Although I present a single test statistic that assesses the overall (global) performance of a phylogenetic model, a variety of test statistics can be tailored to evaluate specific features (local performance) of evolutionary models to identify sources failure. The method presented here, unlike the likelihood-ratio test and parametric bootstrap, accounts for uncertainty in the phylogeny and model parameters.},
url = {https://doi.org/10.1093/oxfordjournals.molbev.a004175},
local-url = {file://localhost/Users/cdunn/Dropbox/articles/Library.papers3/Articles/2002/Bollback/Mol%20Biol%20Evol%202002%20Bollback.pdf},
file = {{Mol Biol Evol 2002 Bollback.pdf:/Users/cdunn/Dropbox/articles/Library.papers3/Articles/2002/Bollback/Mol Biol Evol 2002 Bollback.pdf:application/pdf}},
uri = {\url{papers3://publication/uuid/1034C006-7FD5-4B23-AB57-5C17EBF249BA}}
}



@article{Chang:2015hl,
author = {Chang, E S and Neuhof, M and Rubinstein, N D and Diamant, A and Philippe, H and Huchon, D and Cartwright, P},
title = {{Genomic insights into the evolutionary origin of Myxozoa within Cnidaria}},
journal = {Proceedings of the National Academy of Sciences},
year = {2015},
pages = {1--6},
month = nov,
doi = {10.1073/pnas.1511468112},
language = {English},
read = {Yes},
rating = {0},
date-added = {2015-11-23T17:57:31GMT},
date-modified = {2018-03-22T12:34:48GMT},
url = {https://doi.org/10.1073/pnas.1511468112},
local-url = {file://localhost/Users/cdunn/Dropbox/articles/Library.papers3/Files/36/36C84BEB-BBC5-4A2E-BB05-DC6DD43EF06C.pdf},
file = {{36C84BEB-BBC5-4A2E-BB05-DC6DD43EF06C.pdf:/Users/cdunn/Dropbox/articles/Library.papers3/Files/36/36C84BEB-BBC5-4A2E-BB05-DC6DD43EF06C.pdf:application/pdf;36C84BEB-BBC5-4A2E-BB05-DC6DD43EF06C.pdf:/Users/cdunn/Dropbox/articles/Library.papers3/Files/36/36C84BEB-BBC5-4A2E-BB05-DC6DD43EF06C.pdf:application/pdf}},
uri = {\url{papers3://publication/doi/10.1073/pnas.1511468112}}
}



@article{Feuda:2017ew,
author = {Feuda, Roberto and Dohrmann, Martin and Pett, Walker and Philippe, Hervé and Rota-Stabelli, Omar and Lartillot, Nicolas and Wörheide, Gert and Pisani, Davide},
title = {{Improved Modeling of Compositional Heterogeneity Supports Sponges as Sister to All Other Animals}},
journal = {Current Biology},
year = {2017},
volume = {27},
number = {24},
pages = {1--12},
month = nov,
publisher = {Elsevier Ltd.},
doi = {10.1016/j.cub.2017.11.008},
language = {English},
read = {Yes},
rating = {0},
date-added = {2017-11-30T17:44:47GMT},
date-modified = {2018-06-20T14:37:02GMT},
abstract = {Current Biology, Corrected proof. doi:10.1016/j.cub.2017.11.008},
url = {https://doi.org/10.1016/j.cub.2017.11.008},
local-url = {file://localhost/Users/cdunn/Dropbox/articles/Library.papers3/Files/03/03E86186-0E72-4B49-8578-5B783B2D511B.pdf},
file = {{03E86186-0E72-4B49-8578-5B783B2D511B.pdf:/Users/cdunn/Dropbox/articles/Library.papers3/Files/03/03E86186-0E72-4B49-8578-5B783B2D511B.pdf:application/pdf;03E86186-0E72-4B49-8578-5B783B2D511B.pdf:/Users/cdunn/Dropbox/articles/Library.papers3/Files/03/03E86186-0E72-4B49-8578-5B783B2D511B.pdf:application/pdf}},
uri = {\url{papers3://publication/doi/10.1016/j.cub.2017.11.008}}
}

@article{Foster:2004tw,
author = {Foster, Peter G},
title = {{Modeling compositional heterogeneity.}},
journal = {Systematic biology},
year = {2004},
volume = {53},
number = {3},
pages = {485--495},
month = jun,
affiliation = {Department of Zoology, The Natural History Museum, Cromwell Road, London SW7 5BD, United Kingdom. p.foster@nhm.ac.uk},
pmid = {15503675},
language = {English},
read = {Yes},
rating = {0},
date-added = {2018-06-20T15:00:34GMT},
date-modified = {2018-06-20T15:00:43GMT},
abstract = {Compositional heterogeneity among lineages can compromise phylogenetic analyses, because models in common use assume compositionally homogeneous data. Models that can accommodate compositional heterogeneity with few extra parameters are described here, and used in two examples where the true tree is known with confidence. It is shown using likelihood ratio tests that adequate modeling of compositional heterogeneity can be achieved with few composition parameters, that the data may not need to be modelled with separate composition parameters for each branch in the tree. Tree searching and placement of composition vectors on the tree are done in a Bayesian framework using Markov chain Monte Carlo (MCMC) methods. Assessment of fit of the model to the data is made in both maximum likelihood (ML) and Bayesian frameworks. In an ML framework, overall model fit is assessed using the Goldman-Cox test, and the fit of the composition implied by a (possibly heterogeneous) model to the composition of the data is assessed using a novel tree-and model-based composition fit test. In a Bayesian framework, overall model fit and composition fit are assessed using posterior predictive simulation. It is shown that when composition is not accommodated, then the model does not fit, and incorrect trees are found; but when composition is accommodated, the model then fits, and the known correct phylogenies are obtained.},
url = {https://doi.org/10.1080/10635150490445779},
uri = {\url{papers3://publication/uuid/nr--24E2C9CF-92FE-4289-9366-F6B230B71489}}
}



@article{King:2017ie,
author = {King, Nicole and Rokas, Antonis},
title = {{Embracing Uncertainty in Reconstructing Early Animal Evolution.}},
journal = {Current biology : CB},
year = {2017},
volume = {27},
number = {19},
pages = {R1081--R1088},
month = oct,
affiliation = {Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA. Electronic address: nking@berkeley.edu.},
doi = {10.1016/j.cub.2017.08.054},
pmid = {29017048},
pmcid = {PMC5679448},
language = {English},
read = {Yes},
rating = {0},
date-added = {2018-06-20T14:33:50GMT},
date-modified = {2018-06-20T14:34:30GMT},
abstract = {The origin of animals, one of the major transitions in evolution, remains mysterious. Many key aspects of animal evolution can be reconstructed by comparing living species within a robust phylogenetic framework.~However, uncertainty remains regarding the evolutionary relationships between two ancient animal lineages - sponges and ctenophores - and the remaining animal phyla. Comparative morphology and some phylogenomic analyses support the view that sponges represent the sister lineage to the rest of the animals, while other phylogenomic analyses support ctenophores, a phylum of carnivorous, gelatinous marine organisms, as the sister lineage. Here, we explore why different studies yield different answers and discuss the implications of the two alternative hypotheses for understanding the origin of animals. Reconstruction of ancient evolutionary radiations is devilishly difficult and will likely require broader sampling of sponge and ctenophore genomes, improved analytical strategies and critical analyses of the phylogenetic distribution and molecular mechanisms underlying apparently conserved traits. Rather than staking out positions in favor of the ctenophores-sister or the sponges-sister hypothesis, we submit that research programs aimed at understanding the biology of the first animals should instead embrace the uncertainty surrounding early animal evolution in their experimental designs.},
url = {https://doi.org/10.1016/j.cub.2017.08.054},
local-url = {file://localhost/Users/cdunn/Dropbox/articles/Library.papers3/Files/88/88673B3A-D2DB-47CD-A2DF-FC57E9D8FB9C.pdf},
file = {{88673B3A-D2DB-47CD-A2DF-FC57E9D8FB9C.pdf:/Users/cdunn/Dropbox/articles/Library.papers3/Files/88/88673B3A-D2DB-47CD-A2DF-FC57E9D8FB9C.pdf:application/pdf}},
uri = {\url{papers3://publication/doi/10.1016/j.cub.2017.08.054}}
}


@article{lartillot2009phylobayes,
  title={PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating},
  author={Lartillot, Nicolas and Lepage, Thomas and Blanquart, Samuel},
  journal={Bioinformatics},
  volume={25},
  number={17},
  pages={2286--2288},
  year={2009},
  publisher={Oxford University Press}
}

@article{Lartillot:2013fg,
author = {Lartillot, Nicolas and Rodrigue, Nicolas and Stubbs, Daniel and Richer, Jacques},
title = {{PhyloBayes MPI: phylogenetic reconstruction with infinite mixtures of profiles in a parallel environment.}},
journal = {Systematic biology},
year = {2013},
volume = {62},
number = {4},
pages = {611--615},
month = jul,
publisher = {Oxford University Press},
affiliation = {Centre Robert Cedergren pour la Bioinformatique, D{\'e}partement de Biochimie, Universit{\'e} de Montr{\'e}al, C.P. 6128, Succursale Centre-ville. Montr{\'e}al, Qu{\'e}bec H3C 3J7, Canada. nicolas.lartillot@umontreal.ca},
doi = {10.1093/sysbio/syt022},
pmid = {23564032},
language = {English},
rating = {0},
date-added = {2014-11-21T00:11:50GMT},
date-modified = {2018-06-20T14:58:21GMT},
abstract = {Modeling across site variation of the substitution process is increasingly recognized as important for obtaining more accurate phylogenetic reconstructions. Both finite and infinite mixture models have been proposed and have been shown to significantly improve on classical single-matrix models. Compared with their finite counterparts, infinite mixtures have a greater expressivity. However, they are computationally more challenging. This has resulted in practical compromises in the design of infinite mixture models. In particular, a fast but simplified version of a Dirichlet process model over equilibrium frequency profiles implemented in PhyloBayes has often been used in recent phylogenomics studies, while more refined model structures, more realistic and empirically more fit, have been practically out of reach. We introduce a message passing interface version of PhyloBayes, implementing the Dirichlet process mixture models as well as more classical empirical matrices and finite mixtures. The parallelization is made efficient thanks to the combination of two algorithmic strategies: a partial Gibbs sampling update of the tree topology and the use of a truncated stick-breaking representation for the Dirichlet process prior. The implementation shows close to linear gains in computational speed for up to 64 cores, thus allowing faster phylogenetic reconstruction under complex mixture models. PhyloBayes MPI is freely available from our website www.phylobayes.org.},
url = {https://doi.org/10.1093/sysbio/syt022},
local-url = {file://localhost/Users/cdunn/Dropbox/articles/Library.papers3/Files/94/94A04B5E-75DB-4826-8566-C5EC3C233B20.pdf},
file = {{94A04B5E-75DB-4826-8566-C5EC3C233B20.pdf:/Users/cdunn/Dropbox/articles/Library.papers3/Files/94/94A04B5E-75DB-4826-8566-C5EC3C233B20.pdf:application/pdf}},
uri = {\url{papers3://publication/doi/10.1093/sysbio/syt022}}
}



@article{Susko:2007ds,
author = {Susko, Edward and Roger, Andrew J.},
title = {{On reduced amino acid alphabets for phylogenetic inference}},
journal = {Molecular Biology and Evolution},
year = {2007},
volume = {24},
number = {9},
pages = {2139--2150},
month = sep,
affiliation = {Department of Mathematics and Statistics, Dalhousie University, Halifax, Nova Scotia, Canada. susko@mathstat.dal.ca},
doi = {10.1093/molbev/msm144},
pmid = {17652333},
language = {English},
read = {Yes},
rating = {0},
date-added = {2017-12-15T13:44:44GMT},
date-modified = {2018-06-19T17:04:19GMT},
abstract = {We investigate the use of Markov models of evolution for reduced amino acid alphabets or bins of amino acids. The use of reduced amino acid alphabets can ameliorate effects of model misspecification and saturation. We present algorithms for 2 different ways of automating the construction of bins: minimizing criteria based on properties of rate matrices and minimizing criteria based on properties of alignments. By simulation, we show that in the absence of model misspecification, the loss of information due to binning is found to be insubstantial, and the use of Markov models at the binned level is found to be almost as effective as the more appropriate missing data approach. By applying these approaches to real data sets where compositional heterogeneity and/or saturation appear to be causing biased tree estimation, we find that binning can improve topological estimation in practice.},
url = {https://doi.org/10.1093/molbev/msm144},
local-url = {file://localhost/Users/cdunn/Dropbox/articles/Library.papers3/Files/20/20FF4402-67DD-4554-9DA7-7E837C945AB1.pdf},
file = {{20FF4402-67DD-4554-9DA7-7E837C945AB1.pdf:/Users/cdunn/Dropbox/articles/Library.papers3/Files/20/20FF4402-67DD-4554-9DA7-7E837C945AB1.pdf:application/pdf}},
uri = {\url{papers3://publication/doi/10.1093/molbev/msm144}}
}



@article{Whelan:2015jj,
author = {Whelan, Nathan V and Kocot, Kevin M and Moroz, Leonid L and Halanych, Kenneth M},
title = {{Error, signal, and the placement of Ctenophora sister to all other animals.}},
journal = {Proceedings of the National Academy of Sciences},
year = {2015},
volume = {112},
number = {18},
pages = {201503453--6},
month = apr,
publisher = {National Acad Sciences},
affiliation = {Molette Biology Laboratory for Environmental and Climate Change Studies, Department of Biological Sciences, Auburn University, Auburn, AL 36849; nwhelan@auburn.edu.},
doi = {10.1073/pnas.1503453112},
pmid = {25902535},
language = {English},
read = {Yes},
rating = {0},
date-added = {2015-04-27T14:45:13GMT},
date-modified = {2017-12-10T04:42:31GMT},
abstract = {Elucidating relationships among early animal lineages has been difficult, and recent phylogenomic analyses place Ctenophora sister to all other extant animals, contrary to the traditional view of Porifera as the earliest-branching animal lineage. To date, phylogenetic support for either ctenophores or sponges as sister to other animals has been limited and inconsistent among studies. Lack of agreement among phylogenomic analyses using different data and methods obscures how complex traits, such as epithelia, neurons, and muscles evolved. A consensus view of animal evolution will not be accepted until datasets and methods converge on a single hypothesis of early metazoan relationships and putative sources of systematic error (e.g., long-branch attraction, compositional bias, poor model choice) are assessed. Here, we investigate possible causes of systematic error by expanding taxon sampling with eight novel transcriptomes, strictly enforcing orthology inference criteria, and progressively examining potential causes of systematic error while using both maximum-likelihood with robust data partitioning and Bayesian inference with a site-heterogeneous model. We identified ribosomal protein genes as possessing a conflicting signal compared with other genes, which caused some past studies to infer ctenophores and cnidarians as sister. Importantly, biases resulting from elevated compositional heterogeneity or elevated substitution rates are ruled out. Placement of ctenophores as sister to all other animals, and sponge monophyly, are strongly supported under multiple analyses, herein.},
url = {https://doi.org/10.1073/pnas.1503453112},
local-url = {file://localhost/Users/cdunn/Dropbox/articles/Library.papers3/Files/90/9031AA65-696B-41C7-9C58-4505900885EF.pdf},
file = {{9031AA65-696B-41C7-9C58-4505900885EF.pdf:/Users/cdunn/Dropbox/articles/Library.papers3/Files/90/9031AA65-696B-41C7-9C58-4505900885EF.pdf:application/pdf;9031AA65-696B-41C7-9C58-4505900885EF.pdf:/Users/cdunn/Dropbox/articles/Library.papers3/Files/90/9031AA65-696B-41C7-9C58-4505900885EF.pdf:application/pdf}},
uri = {\url{papers3://publication/doi/10.1073/pnas.1503453112}}
}

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}

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  publisher={Nature Publishing Group}
}

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@article{whelan2016let,
  title={Who let the CAT out of the bag? Accurately dealing with substitutional heterogeneity in phylogenomic analyses},
  author={Whelan, Nathan V and Halanych, Kenneth M},
  journal={Systematic biology},
  volume={66},
  number={2},
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  year={2016},
  publisher={Oxford University Press}
}

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  title={An integrated perspective on phylogenetic workflows},
  author={Guang, August and Zapata, Felipe and Howison, Mark and Lawrence, Charles E and Dunn, Casey W},
  journal={Trends in ecology \& evolution},
  volume={31},
  number={2},
  pages={116--126},
  year={2016},
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}

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  title={Choanoflagellate and choanocyte collar-flagellar systems and the assumption of homology},
  author={Mah, Jasmine L and Christensen-Dalsgaard, Karen K and Leys, Sally P},
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  volume={16},
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  pages={25--37},
  year={2014},
  publisher={Wiley Online Library}
}

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  author={Nielsen, Claus},
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  number={7},
  pages={190638},
  year={2019},
  publisher={The Royal Society}
}

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  title={Cambrian sessile, suspension feeding stem-group ctenophores and evolution of the comb jelly body plan},
  author={Zhao, Yang and Vinther, Jakob and Parry, Luke A and Wei, Fan and Green, Emily and Pisani, Davide and Hou, Xianguang and Edgecombe, Gregory D and Cong, Peiyun},
  journal={Current Biology},
  volume={29},
  number={7},
  pages={1112--1125},
  year={2019},
  publisher={Elsevier}
}

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  title={The genome of the ctenophore Mnemiopsis leidyi and its implications for cell type evolution},
  author={Ryan, Joseph F and Pang, Kevin and Schnitzler, Christine E and Nguyen, Anh-Dao and Moreland, R Travis and Simmons, David K and Koch, Bernard J and Francis, Warren R and Havlak, Paul and Smith, Stephen A and others},
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  volume={342},
  number={6164},
  pages={1242592},
  year={2013},
  publisher={American Association for the Advancement of Science}
}

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  title={Empirical profile mixture models for phylogenetic reconstruction},
  author={Si Quang, Le and Gascuel, Olivier and Lartillot, Nicolas},
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  number={20},
  pages={2317--2323},
  year={2008},
  publisher={Oxford University Press}
}

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  title={Evaluating fast maximum likelihood-based phylogenetic programs using empirical phylogenomic data sets},
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  journal={Molecular biology and evolution},
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  number={2},
  pages={486--503},
  year={2017},
  publisher={Oxford University Press}
}

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  title={IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies},
  author={Nguyen, Lam-Tung and Schmidt, Heiko A and von Haeseler, Arndt and Minh, Bui Quang},
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  volume={32},
  number={1},
  pages={268--274},
  year={2014},
  publisher={Oxford University Press}
}

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  title={Intervene: a tool for intersection and visualization of multiple gene or genomic region sets},
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}