Finish last methodology

[chloroplast13.git] / biblio.bib

diff --git a/biblio.bib b/biblio.bib
index 2225ccf843956e4c3a83b451e9066e16c370c436..d5aaff6a148d3f627a6dd2f673e3f70b28e60b42 100644 (file)
--- a/biblio.bib
+++ b/biblio.bib
@@ -53,6 +53,18 @@ DOI={10.1089/cmb.2010.0092}
   year={2004},
   publisher={Cold Spring Harbor Lab}
 }
   year={2004},
   publisher={Cold Spring Harbor Lab}
 }

+
+@article{chapman2000biopython,
+  title={Biopython: Python tools for computational biology},
+  author={Chapman, Brad and Chang, Jeffrey},
+  journal={ACM SIGBIO Newsletter},
+  volume={20},
+  number={2},
+  pages={15--19},
+  year={2000},
+  publisher={ACM}
+}
+

 @incollection{FI09,
 year={2009},
 isbn={978-3-642-04743-5},
 @incollection{FI09,
 year={2009},
 isbn={978-3-642-04743-5},


@@ -68,6 +80,14 @@ author={Tannier, Eric},
 pages={1-12}
 }
 
 pages={1-12}
 }
 

+@article{gansner2002drawing,
+  title={Drawing graphs with dot},
+  author={Gansner, Emden and Koutsofios, Eleftherios and North, Stephen},
+  journal={Retrieved June},
+  volume={13},
+  pages={2005},
+  year={2002}
+}

 
 @article{10.1371/journal.pone.0052841,
     author = {Blouin, Yann AND Hauck, Yolande AND Soler, Charles AND Fabre, Michel AND Vong, Rithy AND Dehan, Céline AND Cazajous, Géraldine AND Massoure, Pierre-Laurent AND Kraemer, Philippe AND Jenkins, Akinbowale AND Garnotel, Eric AND Pourcel, Christine AND Vergnaud, Gilles},
 
 @article{10.1371/journal.pone.0052841,
     author = {Blouin, Yann AND Hauck, Yolande AND Soler, Charles AND Fabre, Michel AND Vong, Rithy AND Dehan, Céline AND Cazajous, Géraldine AND Massoure, Pierre-Laurent AND Kraemer, Philippe AND Jenkins, Akinbowale AND Garnotel, Eric AND Pourcel, Christine AND Vergnaud, Gilles},


@@ -83,6 +103,32 @@ pages={1-12}
     number = {12},
     doi = {10.1371/journal.pone.0052841}
 }        
     number = {12},
     doi = {10.1371/journal.pone.0052841}
 }        

+
+@article{Sayers01012011,
+author = {Sayers, Eric W. and Barrett, Tanya and Benson, Dennis A. and Bolton, Evan and Bryant, Stephen H. and Canese, Kathi and Chetvernin, Vyacheslav and Church, Deanna M. and DiCuccio, Michael and Federhen, Scott and Feolo, Michael and Fingerman, Ian M. and Geer, Lewis Y. and Helmberg, Wolfgang and Kapustin, Yuri and Landsman, David and Lipman, David J. and Lu, Zhiyong and Madden, Thomas L. and Madej, Tom and Maglott, Donna R. and Marchler-Bauer, Aron and Miller, Vadim and Mizrachi, Ilene and Ostell, James and Panchenko, Anna and Phan, Lon and Pruitt, Kim D. and Schuler, Gregory D. and Sequeira, Edwin and Sherry, Stephen T. and Shumway, Martin and Sirotkin, Karl and Slotta, Douglas and Souvorov, Alexandre and Starchenko, Grigory and Tatusova, Tatiana A. and Wagner, Lukas and Wang, Yanli and Wilbur, W. John and Yaschenko, Eugene and Ye, Jian}, 
+title = {Database resources of the National Center for Biotechnology Information},
+volume = {39}, 
+number = {suppl 1}, 
+pages = {D38-D51}, 
+year = {2011}, 
+doi = {10.1093/nar/gkq1172}, 
+abstract ={In addition to maintaining the GenBank® nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI Web site. NCBI resources include Entrez, the Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central (PMC), Entrez Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Primer-BLAST, COBALT, Electronic PCR, OrfFinder, Splign, ProSplign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, dbVar, Epigenomics, Cancer Chromosomes, Entrez Genomes and related tools, the Map Viewer, Model Maker, Evidence Viewer, Trace Archive, Sequence Read Archive, Retroviral Genotyping Tools, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus (GEO), Entrez Probe, GENSAT, Online Mendelian Inheritance in Man (OMIM), Online Mendelian Inheritance in Animals (OMIA), the Molecular Modeling Database (MMDB), the Conserved Domain Database (CDD), the Conserved Domain Architecture Retrieval Tool (CDART), IBIS, Biosystems, Peptidome, OMSSA, Protein Clusters and the PubChem suite of small molecule databases. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov.}, 
+URL = {http://nar.oxfordjournals.org/content/39/suppl_1/D38.abstract}, 
+eprint = {http://nar.oxfordjournals.org/content/39/suppl_1/D38.full.pdf+html}, 
+journal = {Nucleic Acids Research} 
+}
+
+@article{zafar2002coregenes,
+  title={CoreGenes: A computational tool for identifying and cataloging},
+  author={Zafar, Nikhat and Mazumder, Raja and Seto, Donald},
+  journal={BMC bioinformatics},
+  volume={3},
+  number={1},
+  pages={12},
+  year={2002},
+  publisher={BioMed Central Ltd}
+}
+

 @Article{17623808,
 AUTHOR = {Gomez-Valero, Laura and Rocha, Eduardo P C and Latorre, Amparo and Silva, Francisco J},
 TITLE = {Reconstructing the ancestor of Mycobacterium leprae: the dynamics of gene loss and genome reduction.},
 @Article{17623808,
 AUTHOR = {Gomez-Valero, Laura and Rocha, Eduardo P C and Latorre, Amparo and Silva, Francisco J},
 TITLE = {Reconstructing the ancestor of Mycobacterium leprae: the dynamics of gene loss and genome reduction.},


@@ -122,6 +168,46 @@ NUMBER = {172004},
 PAGES = {3252-3255},
 URL={http://www.biosci.utexas.edu/ib/faculty/jansen/pubs/Wyman%20et%20al.%202004.pdf},
 }
 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},
 @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},


@@ -138,3 +224,20 @@ URL={http://www.biosci.utexas.edu/ib/faculty/jansen/pubs/Wyman%20et%20al.%202004
     number = {7},
     doi = {10.1371/journal.pone.0006291}
 }        
     number = {7},
     doi = {10.1371/journal.pone.0006291}
 }        

+
+@article{altschul1990basic,
+  title={Basic local alignment search tool},
+  author={Altschul, Stephen F and Gish, Warren and Miller, Webb and Myers, Eugene W and Lipman, David J},
+  journal={Journal of molecular biology},
+  volume={215},
+  number={3},
+  pages={403--410},
+  year={1990},
+  publisher={Elsevier}
+}
+
+@article{geneVision,
+  title={DNASTAR- GenVision Software for Genomic Visualizations},
+  author={DNASTAR},
+  url = {http://www.dnastar.com/products/genvision.php} 
+}
\ No newline at end of file