@article{epa,
    author = {Berger, Simon A. and Krompass, Denis and Stamatakis, Alexandros},
    day = {1},
    doi = {10.1093/sysbio/syr010},
    journal = {Systematic Biology},
    month = may,
    number = {3},
    pages = {291--302},
    pmid = {21436105},
    posted-at = {2011-05-24 22:45:36},
    priority = {2},
    title = {{Performance, Accuracy, and Web Server for Evolutionary Placement of Short Sequence Reads under Maximum Likelihood}},
    url = {http://dx.doi.org/10.1093/sysbio/syr010},
    volume = {60},
    year = {2011}
}

@article{pplacer,
    author = {Matsen, Frederick and Kodner, Robin and Armbrust, E. Virginia},
    citeulike-article-id = {8160483},
    citeulike-linkout-0 = {http://dx.doi.org/10.1186/1471-2105-11-538},
    citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/21034504},
    citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=21034504},
    day = {30},
    doi = {10.1186/1471-2105-11-538},
    issn = {1471-2105},
    journal = {BMC Bioinformatics},
    month = oct,
    number = {1},
    pages = {538+},
    pmid = {21034504},
    posted-at = {2011-05-24 22:43:33},
    priority = {2},
    title = {{pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree}},
    url = {http://dx.doi.org/10.1186/1471-2105-11-538},
    volume = {11},
    year = {2010}
}

@article{silberman02,
    abstract = {{We present the first molecular phylogenetic examination of the evolutionary position of retortamonads, a group of mitochondrion-lacking flagellates usually found as commensals of the intestinal tracts of vertebrates. Our phylogenies include small subunit ribosomal gene sequences from six retortamonad isolates—four from mammals and two from amphibians. All six sequences were highly similar (95\%–99\%), with those from mammals being almost identical to each other. All phylogenetic methods utilized unequivocally placed retortamonads with another amitochondriate group, the diplomonads. Surprisingly, all methods weakly supported a position for retortamonads cladistically within diplomonads, as the sister group to Giardia. This position would conflict with a single origin and uniform retention of the doubled-cell organization displayed by most diplomonads, but not by retortamonads. Diplomonad monophyly was not rejected by Shimodaira-Hasegawa, Kishino-Hasegawa, and expected likelihood weights methods but was marginally rejected by parametric bootstrapping. Analyses with additional phylogenetic markers are needed to test this controversial branching order within the retortamonad + diplomonad clade. Nevertheless, the robust phylogenetic association between diplomonads and retortamonads suggests that they share an amitochondriate ancestor. Because strong evidence indicates that diplomonads have secondarily lost their mitochondria (rather than being ancestrally amitochondriate), our results imply that retortamonads are also secondarily amitochondriate. Of the various groups of eukaryotes originally suggested to be primitively amitochondriate under the archezoa hypothesis, all have now been found to have physical or genetic mitochondrial relics (or both) or form a robust clade with an organism with such a relic.}},
    author = {Silberman, Jeffrey D. and Simpson, Alastair G. B. and Kulda, Jaroslav and Cepicka, Ivan and Hampl, Vladimir and Johnson, Patricia J. and Roger, Andrew J.},
    citeulike-article-id = {9263309},
    citeulike-linkout-0 = {http://mbe.oxfordjournals.org/cgi/content/abstract/19/5/777},
    citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/11961110},
    citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=11961110},
    day = {1},
    journal = {Molecular Biology and Evolution},
    month = may,
    number = {5},
    pages = {777--786},
    pmid = {11961110},
    posted-at = {2011-05-07 03:15:02},
    priority = {2},
    title = {{Retortamonad Flagellates are Closely Related to Diplomonads—Implications for the History of Mitochondrial Function in Eukaryote Evolution}},
    url = {http://mbe.oxfordjournals.org/cgi/content/abstract/19/5/777},
    volume = {19},
    year = {2002}
}


@article{Price09,
    abstract = {{Gene families are growing rapidly, but standard methods for inferring phylogenies do not scale to alignments with over 10,000 sequences. We present FastTree, a method for constructing large phylogenies and for estimating their reliability. Instead of storing a distance matrix, FastTree stores sequence profiles of internal nodes in the tree. FastTree uses these profiles to implement neighbor-joining and uses heuristics to quickly identify candidate joins. FastTree then uses nearest-neighbor interchanges to reduce the length of the tree. For an alignment with N sequences, L sites, and a different characters, a distance matrix requires O(N2) space and O(N2L) time, but FastTree requires just O() memory and O() time. To estimate the tree's reliability, FastTree uses local bootstrapping, which gives another 100-fold speedup over a distance matrix. For example, FastTree computed a tree and support values for 158,022 distinct 16S ribosomal RNAs in 17 hours and 2.4 gigabytes of memory. Just computing pairwise Jukes-Cantor distances and storing them, without inferring a tree or bootstrapping, would require 17 hours and 50 gigabytes of memory. In simulations, FastTree was slightly more accurate than neighbor joining, BIONJ, or FastME; on genuine alignments, FastTree's topologies had higher likelihoods. FastTree is available at http://microbesonline.org/fasttree.}},
    author = {Price, Morgan N. and Dehal, Paramvir S. and Arkin, Adam P.},
    citeulike-article-id = {4466193},
    citeulike-linkout-0 = {http://dx.doi.org/10.1093/molbev/msp077},
    citeulike-linkout-1 = {http://mbe.oxfordjournals.org/content/26/7/1641.abstract},
    citeulike-linkout-2 = {http://mbe.oxfordjournals.org/content/26/7/1641.full.pdf},
    citeulike-linkout-3 = {http://mbe.oxfordjournals.org/cgi/content/abstract/26/7/1641?etoc},
    citeulike-linkout-4 = {http://view.ncbi.nlm.nih.gov/pubmed/19377059},
    citeulike-linkout-5 = {http://www.hubmed.org/display.cgi?uids=19377059},
    day = {1},
    doi = {10.1093/molbev/msp077},
    issn = {1537-1719},
    journal = {Molecular Biology and Evolution},
    month = jan,
    number = {7},
    pages = {1641--1650},
    pmid = {19377059},
    posted-at = {2011-04-21 00:52:33},
    priority = {2},
    title = {{FastTree: Computing Large Minimum-Evolution Trees with Profiles instead of a Distance Matrix}},
    url = {http://dx.doi.org/10.1093/molbev/msp077},
    volume = {26},
    year = {2009}
}

@article{greengenes,
    abstract = {{A 16S rRNA gene database (http://greengenes.lbl.gov) addresses limitations of public repositories by providing chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies. It was found that there is incongruent taxonomic nomenclature among curators even at the phylum level. Putative chimeras were identified in 3\% of environmental sequences and in 0.2\% of records derived from isolates. Environmental sequences were classified into 100 phylum-level lineages in the Archaea and Bacteria.}},
    address = {Center for Environmental Biotechnology, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Mail Stop 70A-3317, Berkeley, CA 94720, USA.},
    author = {DeSantis, T. Z. and Hugenholtz, P. and Larsen, N. and Rojas, M. and Brodie, E. L. and Keller, K. and Huber, T. and Dalevi, D. and Hu, P. and Andersen, G. L.},
    citeulike-article-id = {2796059},
    citeulike-linkout-0 = {http://dx.doi.org/10.1128/AEM.03006-05},
    citeulike-linkout-1 = {http://aem.asm.org/cgi/content/abstract/72/7/5069},
    citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/16820507},
    citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=16820507},
    day = {1},
    doi = {10.1128/AEM.03006-05},
    issn = {0099-2240},
    journal = {Appl. Environ. Microbiol.},
    keywords = {greengenes},
    month = jul,
    number = {7},
    pages = {5069--5072},
    pmid = {16820507},
    posted-at = {2011-04-21 00:36:50},
    priority = {2},
    title = {{Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB}},
    url = {http://dx.doi.org/10.1128/AEM.03006-05},
    volume = {72},
    year = {2006}
}

@article{Price10Plos,
    abstract = {{We recently described FastTree, a tool for inferring phylogenies for alignments with up to hundreds of thousands of sequences. Here, we describe improvements to FastTree that improve its accuracy without sacrificing scalability. Where FastTree 1 used nearest-neighbor interchanges (NNIs) and the minimum-evolution criterion to improve the tree, FastTree 2 adds minimum-evolution subtree-pruning-regrafting (SPRs) and maximum-likelihood NNIs. FastTree 2 uses heuristics to restrict the search for better trees and estimates a rate of evolution for each site (the \^{a}CAT\^{a} approximation). Nevertheless, for both simulated and genuine alignments, FastTree 2 is slightly more accurate than a standard implementation of maximum-likelihood NNIs (PhyML 3 with default settings). Although FastTree 2 is not quite as accurate as methods that use maximum-likelihood SPRs, most of the splits that disagree are poorly supported, and for large alignments, FastTree 2 is 100\^{a}1,000 times faster. FastTree 2 inferred a topology and likelihood-based local support values for 237,882 distinct 16S ribosomal RNAs on a desktop computer in 22 hours and 5.8 gigabytes of memory. FastTree 2 allows the inference of maximum-likelihood phylogenies for huge alignments. FastTree 2 is freely available at http://www.microbesonline.org/fasttree.}},
    author = {Price, Morgan N. and Dehal, Paramvir S. and Arkin, Adam P.},
    citeulike-article-id = {6796596},
    citeulike-linkout-0 = {http://dx.doi.org/10.1371/journal.pone.0009490},
    day = {10},
    doi = {10.1371/journal.pone.0009490},
    journal = {PLoS ONE},
    month = mar,
    number = {3},
    pages = {e9490+},
    posted-at = {2011-04-21 00:24:44},
    priority = {2},
    publisher = {Public Library of Science},
    title = {{FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments}},
    url = {http://dx.doi.org/10.1371/journal.pone.0009490},
    volume = {5},
    year = {2010}
}

@article{liu09science,
    abstract = {{Inferring an accurate evolutionary tree of life requires high-quality alignments of molecular sequence data sets from large numbers of species. However, this task is often difficult, slow, and idiosyncratic, especially when the sequences are highly diverged or include high rates of insertions and deletions (collectively known as indels). We present SAT\'{e} (simultaneous alignment and tree estimation), an automated method to quickly and accurately estimate both DNA alignments and trees with the maximum likelihood criterion. In our study, it improved tree and alignment accuracy compared to the best two-phase methods currently available for data sets of up to 1000 sequences, showing that coestimation can be both rapid and accurate in phylogenetic studies.}},
    author = {Liu, Kevin and Raghavan, Sindhu and Nelesen, Serita and Linder, C. Randal and Warnow, Tandy},
    citeulike-article-id = {4900854},
    citeulike-linkout-0 = {http://dx.doi.org/10.1126/science.1171243},
    citeulike-linkout-1 = {http://www.sciencemag.org/content/324/5934/1561.abstract},
    citeulike-linkout-2 = {http://www.sciencemag.org/content/324/5934/1561.full.pdf},
    citeulike-linkout-3 = {http://www.sciencemag.org/cgi/content/abstract/324/5934/1561},
    citeulike-linkout-4 = {http://view.ncbi.nlm.nih.gov/pubmed/19541996},
    citeulike-linkout-5 = {http://www.hubmed.org/display.cgi?uids=19541996},
    day = {19},
    doi = {10.1126/science.1171243},
    journal = {Science},
    keywords = {kevin, science},
    month = jun,
    number = {5934},
    pages = {1561--1564},
    pmid = {19541996},
    posted-at = {2011-04-20 19:05:07},
    priority = {2},
    title = {{Rapid and Accurate Large-Scale Coestimation of Sequence Alignments and Phylogenetic Trees}},
    url = {http://dx.doi.org/10.1126/science.1171243},
    volume = {324},
    year = {2009}
}

@article{phyml,
    author = {Guindon, St\'{e}phane and Dufayard, Jean-Fran\c{c}ois and Lefort, Vincent and Anisimova, Maria and Hordijk, Wim and Gascuel, Olivier},
    day = {1},
    doi = {10.1093/sysbio/syq010},
    journal = {Systematic Biology},
    month = may,
    number = {3},
    pages = {307--321},
    posted-at = {2012-08-02 10:38:18},
    priority = {2},
    title = {New Algorithms and Methods to Estimate {Maximum-Likelihood} Phylogenies: Assessing the Performance of {PhyML} 3.0},
    url = {http://dx.doi.org/10.1093/sysbio/syq010},
    volume = {59},
    year = {2010}
}

@article{hmmer,
  author = {Eddy, Sean R},
  title = {Profile hidden {M}arkov models.},
  journal = {Bioinformatics},
  year = {1998},
  volume = {14},
  pages = {755-763},
  number = {9},
  doi = {10.1093/bioinformatics/14.9.755},
  timestamp = {2011.07.11},
  url = {http://bioinformatics.oxfordjournals.org/content/14/9/755.abstract}
}

@ARTICLE{raxml,
  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},
  pages = {2688-2690},
  number = {21},
  doi = {10.1093/bioinformatics/btl446},
  eprint = {http://bioinformatics.oxfordjournals.org/content/22/21/2688.full.pdf+html},
  timestamp = {2011.05.03},
  url = {http://bioinformatics.oxfordjournals.org/content/22/21/2688.abstract}
}


@Article{liu10Plos,
author = {K. Liu and C.R. Linder and T. Warnow},
title = {Multiple sequence alignment: a major challenge to large-scale
phylogenetics.},
journal = {PLoS Currents},
publisher = {ncbi.nlm.nih.gov},
YEAR = {2010},
PAGES = {RRN1198},
month = {November [revised 2011 March 18]},
PubMedID = {21113338},
ISSN = {2157-3999},
note =  {Version 2},
URL =
{http://www.biomedsearch.com/nih/Multiple-sequence-alignment-major-challenge/211
13338.html}
}

@article{sepp,
author = {Mirarab, Siavash and Nguyen, Nam and Warnow, Tandy},
issn = {17935091},
journal = {Pacific Symposium On Biocomputing},
keywords = {metagenomic analysis,phylogenetic placement},
pages = {247--58},
pmid = {22174280},
title = {{SEPP: SAT\'{e}-Enabled Phylogenetic Placement.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/22174280},
year = {2012}
}

@inproceedings{metaphyler,
author = {Liu, Bo and Gibbons, Theodore and Ghodsi, Mohammad and Pop, Mihai},
booktitle = {Bioinformatics and Biomedicine (BIBM), 2010 IEEE International Conference on},
isbn = {9781424483051},
keywords = {-metagenomics,phylogenetic,taxonomic profiling},
pages = {95--100},
publisher = {IEEE},
title = {{MetaPhyler: Taxonomic profiling for metagenomic sequences}},
url = {http://ieeexplore.ieee.org/xpls/abs\_all.jsp?arnumber=5706544},
year = {2011}
}

@article{sate2,
author = {Liu, Kevin and Warnow, Tandy J and Holder, Mark T and Nelesen, Serita M and Yu, Jiaye and Stamatakis, Alexandros P and Linder, C Randal},
doi = {10.1093/sysbio/syr095},
institution = {Department of Computer Science, University of Texas at Austin, Austin, TX 78712, USA.},
issn = {1076836X},
journal = {Systematic Biology},
number = {1},
pages = {90--106},
pmid = {22139466},
publisher = {OXFORD UNIV PRESS},
title = {{SATe-II: Very Fast and Accurate Simultaneous Estimation of Multiple Sequence Alignments and Phylogenetic Trees.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/22139466},
volume = {61},
year = {2011}
}

@article{pasta-jcb,
	annote = {{\{}:PMCID:PMC4424971{\}}},
	author = {Mirarab, Siavash and Nguyen, Nam and Guo, Sheng and Wang, Li-San and Kim, Junhyong and Warnow, Tandy},
	doi = {10.1089/cmb.2014.0156},
	file = {:Users/smirarab/Research/papers/2015 - Journal of Computational Biology - Mirarab et al.pdf:pdf;:Users/smirarab/Research/papers/Supp{\_}Data.pdf:pdf},
	issn = {1066-5277},
	journal = {Journal of Computational Biology},
	keywords = {1,algorithms,function of rnas and,in many bioinformatics analyses,including,introduction and motivation,is a basic step,metagenomics,molecular evolution,msa,multiple alignment,performance,phylogenetic trees,predicting the structure and,proteins and estimating phylogenies,ultiple sequence alignment},
	mendeley-groups = {comprehensive,mine},
	number = {05},
	pages = {377--386},
	title = {{PASTA: Ultra-Large Multiple Sequence Alignment for Nucleotide and Amino-Acid Sequences}},
	url = {http://online.liebertpub.com/doi/abs/10.1089/cmb.2014.0156},
	volume = {22},
	year = {2015}
} 
