Update the section of dogma annotation

[chloroplast13.git] / biblio.bib

diff --git a/biblio.bib b/biblio.bib
index 2225ccf843956e4c3a83b451e9066e16c370c436..e3497026da5a95fdc45b53c085ed9d8e740e4e32 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 +103,18 @@ pages={1-12}
     number = {12},
     doi = {10.1371/journal.pone.0052841}
 }        
     number = {12},
     doi = {10.1371/journal.pone.0052841}
 }        

+
+@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 +154,46 @@ 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 +210,20 @@ 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