[adegenet-commits] r965 - www
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sat Oct 15 19:46:22 CEST 2011
Author: jombart
Date: 2011-10-15 19:46:21 +0200 (Sat, 15 Oct 2011)
New Revision: 965
Modified:
www/literature.html
Log:
+1ref
Modified: www/literature.html
===================================================================
--- www/literature.html 2011-10-10 09:25:56 UTC (rev 964)
+++ www/literature.html 2011-10-15 17:46:21 UTC (rev 965)
@@ -1,583 +1,763 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
-<html>
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- <meta content="text/html; charset=ISO-8859-1"
- http-equiv="content-type">
- <title>documentation</title>
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+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+<html>
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+ <meta content="text/html; charset=ISO-8859-1"
+ http-equiv="content-type">
+ <title>documentation</title>
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+
+ </script>
+ </head>
+ <body>
+ <br>
+ <br>
+ <br>
+ <div style="margin-left: 40px;"><span style="text-decoration:
+ underline;">To cite adegenet:</span><br>
+ <br>
+ <span style="color: rgb(0, 153, 0);">Jombart T</span><span
+ style="color: rgb(0, 153, 0);">.</span><span style="color:
+ rgb(0, 153, 0);"> (</span><span style="font-style: italic;
+ color: rgb(0, 153, 0);"></span><span style="color: rgb(0, 153,
+ 0);">2008)</span><span style="font-weight: bold; color: rgb(0,
+ 153, 0);"> </span><span style="color: rgb(0, 153, 0);">adegenet:
+ a R package for the
+ multivariate analysis of genetic markers. </span><span
+ style="font-style: italic; color: rgb(0, 153, 0);">Bioinformatics</span><span
+ style="color: rgb(0, 153, 0);"> </span><span
+ style="font-weight: bold; color: rgb(0, 153, 0);">24</span><span
+ style="color: rgb(0, 153, 0);">: 1403-1405. doi:
+ 10.1093/bioinformatics/btn129 [</span><a style="color: rgb(0,
+ 153, 0);"
+href="http://bioinformatics.oxfordjournals.org/cgi/reprint/btn129?ijkey=6sqx5BTXCdYtBZz&keytype=ref">link</a><span
+ style="color: rgb(0, 153, 0);"> to a free pdf]</span><br>
+ <br>
+ <span style="color: rgb(0, 153, 0);">Jombart T. and Ahmed I.
+ (2011) </span><span style="font-style: italic; color: rgb(0,
+ 153, 0);">adegenet 1.3-1</span><span style="color: rgb(0, 153,
+ 0);">: new tools for the analysis of
+ genome-wide SNP data. </span><span style="font-style: italic;
+ color: rgb(0, 153, 0);">Bioinformatics</span><span style="color:
+ rgb(0, 153, 0);">. doi: 10.1093/bioinformatics/btr521 [</span><a
+ style="color: rgb(0, 153, 0);"
+href="http://bioinformatics.oxfordjournals.org/content/early/2011/09/16/bioinformatics.btr521">link
- var _gaq = _gaq || [];
- _gaq.push(['_setAccount', 'UA-20083187-1']);
- _gaq.push(['_trackPageview']);
- (function() {
- var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
- ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
- var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
- })();
- </script>
-</head>
-<body>
-<br>
-<br>
-<br>
-<div style="margin-left: 40px;"><span
- style="text-decoration: underline;">To cite adegenet:</span><br>
-<br>
-<span style="color: rgb(0, 153, 0);">Jombart T</span><span
- style="color: rgb(0, 153, 0);">.</span><span
- style="color: rgb(0, 153, 0);"> (</span><span
- style="font-style: italic; color: rgb(0, 153, 0);"></span><span
- style="color: rgb(0, 153, 0);">2008)</span><span
- style="font-weight: bold; color: rgb(0, 153, 0);"> </span><span
- style="color: rgb(0, 153, 0);">adegenet: a R package for the
-multivariate analysis of genetic markers. </span><span
- style="font-style: italic; color: rgb(0, 153, 0);">Bioinformatics</span><span
- style="color: rgb(0, 153, 0);"> </span><span
- style="font-weight: bold; color: rgb(0, 153, 0);">24</span><span
- style="color: rgb(0, 153, 0);">: 1403-1405. doi:
-10.1093/bioinformatics/btn129 [</span><a style="color: rgb(0, 153, 0);"
- href="http://bioinformatics.oxfordjournals.org/cgi/reprint/btn129?ijkey=6sqx5BTXCdYtBZz&keytype=ref">link</a><span
- style="color: rgb(0, 153, 0);"> to a free pdf]</span><br>
-<br>
-<span style="color: rgb(0, 153, 0);">Jombart T. and Ahmed I. (2011) </span><span
- style="font-style: italic; color: rgb(0, 153, 0);">adegenet 1.3-1</span><span
- style="color: rgb(0, 153, 0);">: new tools for the analysis of
-genome-wide SNP data. </span><span
- style="font-style: italic; color: rgb(0, 153, 0);">Bioinformatics</span><span
- style="color: rgb(0, 153, 0);">. doi: 10.1093/bioinformatics/btr521 [</span><a
- style="color: rgb(0, 153, 0);"
- href="http://bioinformatics.oxfordjournals.org/content/early/2011/09/16/bioinformatics.btr521">link
+to
+ the bublisher's website</a><span style="color: rgb(0, 153, 0);">]</span>
+ <img style="width: 80px; height: 37px;" alt=""
+ src="images/new.png"><br style="color: rgb(0, 153, 0);">
+ <br>
+ <br style="color: rgb(0, 153, 0);">
+ <br>
+ <span style="text-decoration: underline;">Related publications:<br>
+ <br style="text-decoration: underline;">
+ </span>- a review of applications of multivariate analyses to
+ genetic
+ markers data:<br>
+ <b>Jombart T</b>, Pontier D, Dufour AB. (2009) <span
+ style="font-style: italic;"></span> Genetic markers in the
+ playground
+ of multivariate analysis. <span style="font-style: italic;">Heredity
+ </span><span style="font-weight: bold;">102</span>: 330-341.
+ doi:10.1038/hdy.2008.130<span style="font-style: italic;">. </span>[<a
+href="http://www.nature.com/hdy/journal/vaop/ncurrent/pdf/hdy2008130a.pdf">link</a>
+ to the journal's pdf - <a target="_new"
+href="http://www.nature.com/hdy/journal/vaop/ncurrent/abs/hdy2008130a.html">free
+ abstract</a>]<br>
+ <br>
+ - the paper presenting the <span style="font-style: italic;">spatial
+principal
+ component analysis</span> (<span style="font-style: italic;">sPCA</span>,
+ function <span style="font-family: monospace; color: rgb(255, 0,
+ 0);">spca</span>),
+ global and local tests (<span style="font-family: monospace;
+ color: rgb(255, 0, 0);">global.rtest</span>
+ and <span style="font-family: monospace; color: rgb(255, 0, 0);">local.rtest</span>):<br>
+ <b>Jombart T, </b>Devillard S, Dufour AB, Pontier D<b> </b>(2008)<b>
+ </b>Revealing
+ cryptic spatial patterns in genetic variability by a new
+ multivariate
+ method. <span style="font-style: italic;">Heredity</span> <span
+ style="font-weight: bold;">101</span>: 92-103. doi:
+ 10.1038/hdy.2008.34 [<a
+href="http://www.nature.com/hdy/journal/vaop/ncurrent/pdf/hdy200834a.pdf">link</a>
+ on the journal's website - <a target="_new"
+href="http://www.nature.com/hdy/journal/vaop/ncurrent/abs/hdy200834a.html">free
+ abstract</a>]<br>
+ </div>
+ <br>
+ <div style="margin-left: 40px;"><span style="font-family: monospace;
+ font-weight: bold;"></span><span style="font-family: monospace;
+ font-weight: bold;"></span>- the paper
+ presenting the <span style="font-style: italic;">SeqTrack </span>algorithm
+ (<span style="font-family: monospace; color: rgb(255, 0, 0);">seqTrack</span>),
-to the bublisher's website</a><span style="color: rgb(0, 153, 0);">]</span>
-<img style="width: 80px; height: 37px;" alt="" src="images/new.png"><br
- style="color: rgb(0, 153, 0);">
-<br>
-<br style="color: rgb(0, 153, 0);">
-<br>
-<span style="text-decoration: underline;">Related publications:<br>
-<br style="text-decoration: underline;">
-</span>- a review of applications of multivariate analyses to genetic
-markers data:<br>
-<b>Jombart T</b>, Pontier D, Dufour AB. (2009) <span
- style="font-style: italic;"></span> Genetic markers in the playground
-of multivariate analysis. <span style="font-style: italic;">Heredity </span><span
- style="font-weight: bold;">102</span>: 330-341.
-doi:10.1038/hdy.2008.130<span style="font-style: italic;">. </span>[<a
- href="http://www.nature.com/hdy/journal/vaop/ncurrent/pdf/hdy2008130a.pdf">link</a>
-to the journal's pdf - <a target="_new"
- href="http://www.nature.com/hdy/journal/vaop/ncurrent/abs/hdy2008130a.html">free
+and
+ simulations of genealoies of haplotypes (<span style="font-family:
+ monospace; color: rgb(255, 0, 0);">haploGen</span>):<br>
+ <b>Jombart T, </b>Eggo RM, Dodd PJ, Balloux F (2010)
+ Reconstructing
+ disease outbreaks from genetic data: a graph approach. <span
+ style="font-style: italic;">Heredity</span>. Doi:
+ 10.1038/hdy.2010.78<br>
+ <br>
+ - the paper introducing the <span style="font-style: italic;">Discriminant
-abstract</a>]<br>
-<br>
-- the paper presenting the <span style="font-style: italic;">spatial
-principal component analysis</span> (<span style="font-style: italic;">sPCA</span>,
-function <span style="font-family: monospace; color: rgb(255, 0, 0);">spca</span>),
-global and local tests (<span
- style="font-family: monospace; color: rgb(255, 0, 0);">global.rtest</span>
-and <span style="font-family: monospace; color: rgb(255, 0, 0);">local.rtest</span>):<br>
-<b>Jombart T, </b>Devillard S, Dufour AB, Pontier D<b> </b>(2008)<b> </b>Revealing
-cryptic spatial patterns in genetic variability by a new multivariate
-method. <span style="font-style: italic;">Heredity</span> <span
- style="font-weight: bold;">101</span>: 92-103. doi:
-10.1038/hdy.2008.34 [<a
- href="http://www.nature.com/hdy/journal/vaop/ncurrent/pdf/hdy200834a.pdf">link</a>
-on the journal's website - <a target="_new"
- href="http://www.nature.com/hdy/journal/vaop/ncurrent/abs/hdy200834a.html">free
-
-
-
-
-abstract</a>]<br>
-</div>
-<br>
-<div style="margin-left: 40px;"><span
- style="font-family: monospace; font-weight: bold;"></span><span
- style="font-family: monospace; font-weight: bold;"></span>- the paper
-presenting the <span style="font-style: italic;">SeqTrack </span>algorithm
-(<span style="font-family: monospace; color: rgb(255, 0, 0);">seqTrack</span>),
-
-
-
-
-and simulations of genealoies of haplotypes (<span
- style="font-family: monospace; color: rgb(255, 0, 0);">haploGen</span>):<br>
-<b>Jombart T, </b>Eggo RM, Dodd PJ, Balloux F (2010) Reconstructing
-disease outbreaks from genetic data: a graph approach. <span
- style="font-style: italic;">Heredity</span>. Doi: 10.1038/hdy.2010.78<br>
-<br>
-- the paper introducing the <span style="font-style: italic;">Discriminant
-
-
-
-
-Analysis of Principal Components</span> (<span
- style="font-style: italic;">DAPC</span>, functions <span
- style="font-family: monospace;"><span style="color: rgb(255, 0, 0);">find.clusters</span>
-</span>and <span style="font-family: monospace; color: rgb(255, 0, 0);">dapc</span>):<img
- style="width: 80px; height: 37px;" alt="" src="images/new.png"><br>
-<b>Jombart T</b>, Devillard S and Balloux F <b> </b>(2010)
-Discriminant analysis of principal components: a new method for the
-analysis of genetically structured populations. <i>BMC Genetics</i> <strong>11</strong><strong>:</strong>94.
-<span>doi:10.1186/1471-2156-11-94</span> [<a href="files/DAPCpaper.pdf">free
-pdf</a>] [<a href="http://www.biomedcentral.com/1471-2156/11/94">free
-html version</a>] [<a href="reviewDAPC.html">evaluation by Laurent
-Excoffier on F1000</a>] <br>
-<br>
-<br>
-<br>
-<span style="text-decoration: underline;">Publications citing adegenet:</span><br
- style="text-decoration: underline;">
-<br>
-[1] Cohas A, Yoccoz NG, Bonenfant C, Goossens B, Genton C, Galan M,
-Kempenaers B, Allainé D (2007) The<span
- style="color: rgb(0, 0, 0);"> genetic similarity between pair members
-influences the frequency of extrapair paternity in alpine marmots</span>.
-<i>Animal Behaviour</i><i> </i><span style="font-weight: bold;">76</span>:
-87-95.<br>
-<br>
-[2] Satkoski JA, Malhi RS, Kanthaswamy S, Tito RY, Malladi VS,
-Smith DG (2008) Pyrosequencing as a method for SNP identification in
-the rhesus macaque (<em>Macaca mulatta</em>). <span
- class="citation-abbreviation"><span style="font-style: italic;">BMC
-Genomics</span></span><span class="citation-publication-date"> </span><span
- style="font-weight: bold;" class="citation-volume">9</span><span
- class="citation-issue"></span>: 256.<br>
-<div><span class="citation-flpages"><br>
-[3] </span>Kanthaswamy S, Satkoski J, George D, Kou A, Erickson BJ,
-Smith DG. (2008). Interspecies hybridization and the stratification of
-nuclear genetic variation of rhesus (<span style="font-style: italic;">Macaca
-mulatta</span>) and long-tailed macaques (<span
- style="font-style: italic;">Macaca </span><span
- style="font-style: italic;">fascicularis</span>). <span
- style="font-style: italic;">Int J Primatol</span> <span
- style="font-weight: bold;">29</span>: 1295-1311.<br>
-<br>
-[4] Kidd, AG, Bowman J, Lesbarrères D, Schulte-Hostedde AI
-(2009). Hybridization between escaped domestic and wild American mink (<span
- style="font-style: italic;">Neovison vison</span>). <span
- style="font-style: italic;">Molecular Ecology</span> <span
- style="font-weight: bold;">18</span>: 1175-1186.<br>
-<br>
-[5] Cohas E, Bonenfant C, Kempaners B, Allainé D (2009).
-Age-specific effect of heterozygosity on survival in alpine marmots, <span
- class="i"><span style="font-style: italic;">Marmota marmota</span>.</span><span
- style="font-style: italic;"> Molecular Ecology</span> <span
- style="font-weight: bold;">18</span>: 1491-1503.<br>
-<br>
-[6] O'Brien J, Devillard S, Say L, Vanthomme A, Léger F, Ruette
-S, Pontier D (2009). Preserving genetic integrity in a hybridising
-world:<br>
-are European Wildcats (<span style="font-style: italic;">Felis
-silvestris silvestris</span>) in eastern France distinct from sympatric
-feral domestic cats? <span style="font-style: italic;">Biodivers
-Conserv</span> <span style="font-weight: bold;">18</span>: 2351-2360.<br>
-<br>
-[7] Kanthaswamy S <span style="font-style: italic;">et al.</span>
-(2009). Canine Population Data Generated from a Multiplex STR Kit for
-Use in Forensic Casework. <span style="font-style: italic;">Journal of
-Forensic Sciences</span> <span style="font-weight: bold;">54</span>:
-829-840.<br>
-<br>
-[8] Lankau R A, Nuzzo V, Spyreas G, Davis A S (2009). Evolutionary
-limits ameliorate the negative impact of an invasive plant. <span
- style="font-style: italic;">Proceedings of the National Academy of
-Sciences</span> <span style="font-weight: bold;">106</span>:
-15362-15367.<br>
-<br>
-[9] Dutech C, Fabreguettes O, Capdevielle X, Robin C (2009) Multiple
-introductions of divergent genetic lineages in an invasive fungal
-pathogen, Cryphonectria parasitica, in France. <span
- style="font-style: italic;">Heredity</span> (advanced online) doi:
-10.1038/hdy.2009.164.<br>
-<br>
-[10] L Y Rutledge, C J Garroway, K M Loveless and B
-R Patterson (2010) Genetic differentiation of eastern wolves in
-Algonquin Park despite bridging gene flow between coyotes and grey
-wolves.<span style="font-style: italic;"> Heredity</span> (advanced
-online) doi: 10.1038/hdy.2010.6.<br>
-<br>
-[11] Jennifer Paul, Nicole Vachon,
-Colin J. Garroway and Joanna R. Freeland (2010)
-Molecular data provide strong evidence of natural hybridization between
-native and introduced lineages of <i>Phragmites australis</i> in North
-America. <span style="font-style: italic;">Biological Invasions</span>.
-doi: 10.1007/s10530-010-9699-6.<br>
-<br>
-[12] C. BERTHOULY, D. DO NGOC, S. THÉVENON, D. BOUCHEL, T. NHU
-VAN, C. DANES, V. GROSBOIS, H. HOANG THANH, C. VU CHI, J.-C. MAILLARD
-(2009) How does farmer connectivity influence livestock genetic
-structure? A case-study in a Vietnamese goat population. <span
- style="font-style: italic;">Molecular Ecology</span> <span
- style="font-weight: bold;">18</span>: 3980-3991<br>
-<br>
-[13] <span class="name"><span class="forenames">COLIN J.</span> <span
- class="surname">GARROWAY</span><sup><nobr></nobr></sup></span>, <span
- class="name"><span class="forenames">JEFF</span> <span class="surname">BOWMAN</span></span>,
-<span class="name"><span class="forenames">TARA J.</span> <span
- class="surname">CASCADEN</span></span>, <span class="name"><span
- class="forenames">GILLIAN L.</span> <span class="surname">HOLLOWAY</span></span>,
-<span class="name"><span class="forenames">CAROLYN G.</span> <span
- class="surname">MAHAN</span></span>, <span class="name"><span
- class="forenames">JAY R.</span> <span class="surname">MALCOLM</span></span>,
-<span class="name"><span class="forenames">MICHAEL A.</span> <span
- class="surname">STEELE</span><sup><nobr></nobr></sup></span>, <span
- class="name"><span class="forenames">GREGORY</span> <span
- class="surname">TURNER</span></span> and <span class="name"><span
- class="forenames">PAUL J.</span> <span class="surname">WILSON</span>
-(2009) </span>Climate change induced hybridization in flying
-squirrels. <span style="font-style: italic;">Global Change Biology</span>
-<span style="font-weight: bold;">16</span>: 113-121.<br>
-<br>
-[14] <span class="name"><span class="forenames">JOSSELIN</span> <span
- class="surname">MONTARRY</span></span>, <span class="name"><span
- class="forenames">DIDIER</span> <span class="surname">ANDRIVON</span>,</span>
-<span class="name"><span class="forenames">ISABELLE</span> <span
- class="surname">GLAIS</span></span>, <span class="name"><span
- class="forenames">ROSELYNE</span> <span class="surname">CORBIERE</span></span>,
-<span class="name"><span class="forenames">GLADYS</span> <span
- class="surname">MIALDEA</span></span> and <span class="name"><span
- class="forenames">FRANCOIS</span> <span class="surname">DELMOTTE
-(2010)</span></span> Microsatellite markers reveal two admixed genetic
-groups and an ongoing displacement within the French population of the
-invasive plant pathogen <span class="i"><span
- style="font-style: italic;">Phytophthora infestans</span>. <span
- style="font-style: italic;">Molecular Ecology</span> <span
- style="font-weight: bold;">19</span>: <span
- style="text-decoration: underline;"></span></span>1965-1977<br>
-<br>
-[15] Gwenaelle Comont, Marie-France Corio-Costet,
-Philippe Larignon and François Delmotte (2010) AFLP
-markers reveal two genetic groups in the French population of the
-grapevine fungal pathogen <i>Phaeomoniella chlamydospora. European
-Journal of Plant Pathology</i> Doi: 10.1007/s10658-010-9611-3<br>
-<br>
-[16] <span class="name"><span class="forenames">Michelle F.</span> <span
- class="surname">DiLeo</span></span>, <span class="name"><span
- class="forenames">Jeffrey R.</span> <span class="surname">Row</span></span>
-and <span class="name"><span class="forenames">Stephen C.</span> <span
- class="surname">Lougheed (2010)</span></span> Discordant patterns of
-population structure for two co-distributed snake species across a
-fragmented Ontario landscape. <span style="font-style: italic;">Diversity
-and Distributions.</span> Doi: <span class="doi">10.1111/j.1472-4642.2010.00667.x<br>
-<br>
-[17] </span><span class="name"><span class="forenames">Francisco</span>
-<span class="surname">Balao</span><sup><nobr></nobr></sup></span>, <span
- class="name"><span class="forenames">Luis M.</span> <span
- class="surname">Valente</span><sup><nobr></nobr></sup></span>, <span
- class="name"><span class="forenames">Pablo</span> <span
- class="surname">Vargas</span><sup><nobr></nobr></sup> </span>, <span
- class="name"><span class="forenames">Javier</span> <span
- class="surname">Herrera</span><sup><nobr></nobr></sup> </span> and <span
- class="name"><span class="forenames">Salvador</span> <span
- class="surname">Talavera</span> (2010)</span> Radiative evolution of
-polyploid races of the Iberian carnation <span class="i">Dianthus
-broteri</span> (Caryophyllaceae).<span class="name"> <sup
- style="font-style: italic;"><nobr></nobr></sup></span><span class="doi"><span
- style="font-style: italic;">New Phytologist. </span>Doi:</span><span
- class="doi"> 10.1111/j.1469-8137.2010.03280.x<br>
-<br>
-[18] </span>Gadieux P, Caffier V , Devaux M , Le Cam B(2010)
-Host-specific differentiation among populations of Venturia inaegualis
-causing scab on apple, pyracantha and loquat. <span
- style="font-style: italic;">FUNGAL GENETICS AND BIOLOGY</span> ,
-47: 511-521<br>
-<span style="display: block;" id="records_chunks"><br>
-[19] Joost S, Colli L, Baret PV, et al. (2010) Integrating
-geo-referenced multiscale and multidisciplinary data for the management
-of biodiversity in livestock genetic resources. <span
- style="font-style: italic;">Animal Genetics </span><span
- style="font-weight: bold;">41</span>: 47-63.<br>
- </span><span class="authors"><span style="white-space: nowrap;">[20]
-Denis Laloë</span>, <span style="white-space: nowrap;">Katayoun
-Moazami-Goudarzi</span>, <span style="white-space: nowrap;">Johannes
-A. Lenstra</span>, <span style="white-space: nowrap;">Paolo Ajmone
-Marsan</span>, <span style="white-space: nowrap;">Pedro Azor</span>, <span
- style="white-space: nowrap;">Roswitha Baumung</span>, <span
- style="white-space: nowrap;">Daniel G. Bradley</span>, <span
- style="white-space: nowrap;">Michael W. Bruford</span>, <span
- style="white-space: nowrap;">Javier Cañón</span>, <span
- style="white-space: nowrap;">Gaudenz Dolf</span>, <span
- style="white-space: nowrap;">Susana Dunner</span>, <span
- style="white-space: nowrap;">Georg Erhardt</span>, <span
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