+}
+@article{Eisen2007,
+ author = {Eisen, Jonathan A},
+ journal = {PLoS Biol},
+ publisher = {Public Library of Science},
+ title = {Environmental Shotgun Sequencing: Its Potential and Challenges for Studying the Hidden World of Microbes},
+ year = {2007},
+ month = {03},
+ volume = {5},
+ url = {http://dx.doi.org/10.1371%2Fjournal.pbio.0050082},
+ pages = {e82},
+ abstract = {
+ <p>Environmental shotgun sequencing promises to reveal novel and fundamental insights into the hidden world of microbes, but the complexity of analysis required to realize this potential poses unique interdisciplinary challenges.</p>
+ },
+ number = {3},
+ doi = {10.1371/journal.pbio.0050082}
+}
+@Article{RDogma,
+AUTHOR = {Stacia K. Wyman, Robert K. Jansen and Jeffrey L. Boore},
+TITLE = {Automatic annotation of organellar genomes
+with DOGMA},
+JOURNAL = {BIOINFORMATICS, oxford Press},
+VOLUME = {20},
+YEAR = {2004},
+NUMBER = {172004},
+PAGES = {3252-3255},
+URL={http://www.biosci.utexas.edu/ib/faculty/jansen/pubs/Wyman%20et%20al.%202004.pdf},
+}
+@article{guindon2005phyml,
+ title={PHYML Online—a web server for fast maximum likelihood-based phylogenetic inference},
+ author={Guindon, Stephane and Lethiec, Franck and Duroux, Patrice and Gascuel, Olivier},
+ journal={Nucleic acids research},
+ volume={33},
+ number={suppl 2},
+ pages={W557--W559},
+ year={2005},
+ publisher={Oxford Univ Press}
+}
+
+@article{goloboff2008tnt,
+ title={TNT, a free program for phylogenetic analysis},
+ author={Goloboff, Pablo A and Farris, James S and Nixon, Kevin C},
+ journal={Cladistics},
+ volume={24},
+ number={5},
+ pages={774--786},
+ year={2008},
+ publisher={Wiley Online Library}
+}
+
+@article{stamatakis2008raxml,
+ title={The RAxML 7.0. 4 Manual},
+ author={Stamatakis, Alexandros},
+ journal={Department of Computer Science. Ludwig-Maximilians-Universit{\"a}t M{\"u}nchen},
+ year={2008}
+}
+@article{stamatakis2005raxml,
+ title={RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees},
+ author={Stamatakis, Alexandros and Ludwig, Thomas and Meier, Harald},
+ journal={Bioinformatics},
+ volume={21},
+ number={4},
+ pages={456--463},
+ year={2005},
+ publisher={Oxford Univ Press}
+}
+
+
+@article{Bakke2009,
+ author = {Bakke, Peter AND Carney, Nick AND DeLoache, Will AND Gearing, Mary AND Ingvorsen, Kjeld AND Lotz, Matt AND McNair, Jay AND Penumetcha, Pallavi AND Simpson, Samantha AND Voss, Laura AND Win, Max AND Heyer, Laurie J. AND Campbell, A. Malcolm},
+ journal = {PLoS ONE},
+ publisher = {Public Library of Science},
+ title = {Evaluation of Three Automated Genome Annotations for <italic>Halorhabdus utahensis</italic>},
+ year = {2009},
+ month = {07},
+ volume = {4},
+ url = {http://dx.doi.org/10.1371%2Fjournal.pone.0006291},
+ pages = {e6291},
+ abstract = {
+<p>Genome annotations are accumulating rapidly and depend heavily on automated annotation systems. Many genome centers offer annotation systems but no one has compared their output in a systematic way to determine accuracy and inherent errors. Errors in the annotations are routinely deposited in databases such as NCBI and used to validate subsequent annotation errors. We submitted the genome sequence of halophilic archaeon <italic>Halorhabdus utahensis</italic> to be analyzed by three genome annotation services. We have examined the output from each service in a variety of ways in order to compare the methodology and effectiveness of the annotations, as well as to explore the genes, pathways, and physiology of the previously unannotated genome. The annotation services differ considerably in gene calls, features, and ease of use. We had to manually identify the origin of replication and the species-specific consensus ribosome-binding site. Additionally, we conducted laboratory experiments to test <italic>H. utahensis</italic> growth and enzyme activity. Current annotation practices need to improve in order to more accurately reflect a genome's biological potential. We make specific recommendations that could improve the quality of microbial annotation projects.</p>
+},
+ number = {7},
+ doi = {10.1371/journal.pone.0006291}
+}
