<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=Windows-1252">
<meta name="Generator" content="Microsoft Word 15 (filtered medium)">
<!--[if !mso]><style>v\:* {behavior:url(#default#VML);}
o\:* {behavior:url(#default#VML);}
w\:* {behavior:url(#default#VML);}
.shape {behavior:url(#default#VML);}
</style><![endif]--><style><!--
/* Font Definitions */
@font-face
{font-family:"Cambria Math";
panose-1:2 4 5 3 5 4 6 3 2 4;}
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
@font-face
{font-family:Tahoma;
panose-1:2 11 6 4 3 5 4 4 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0cm;
margin-bottom:.0001pt;
font-size:11.0pt;
font-family:"Calibri",sans-serif;}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:#0563C1;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:#954F72;
text-decoration:underline;}
p
{mso-style-priority:99;
mso-margin-top-alt:auto;
margin-right:0cm;
mso-margin-bottom-alt:auto;
margin-left:0cm;
font-size:12.0pt;
font-family:"Times New Roman",serif;}
p.msochpdefault, li.msochpdefault, div.msochpdefault
{mso-style-name:msochpdefault;
mso-style-priority:99;
mso-margin-top-alt:auto;
margin-right:0cm;
mso-margin-bottom-alt:auto;
margin-left:0cm;
font-size:12.0pt;
font-family:"Calibri",sans-serif;}
span.emailstyle17
{mso-style-name:emailstyle17;
font-family:"Calibri",sans-serif;
color:windowtext;}
span.EmailStyle20
{mso-style-type:personal;
font-family:"Calibri",sans-serif;
color:#1F497D;}
span.EmailStyle22
{mso-style-type:personal-reply;
font-family:"Calibri",sans-serif;
color:#1F497D;}
.MsoChpDefault
{mso-style-type:export-only;
font-size:10.0pt;}
@page WordSection1
{size:612.0pt 792.0pt;
margin:72.0pt 72.0pt 72.0pt 72.0pt;}
div.WordSection1
{page:WordSection1;}
--></style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]-->
</head>
<body lang="EN-GB" link="#0563C1" vlink="#954F72">
<div class="WordSection1">
<p class="MsoNormal"><span style="color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<div>
<p class="MsoNormal"><span style="color:#2E74B5">Robert Fairweather<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#2E74B5">Research Student<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#2E74B5">Molecular Ecology and Fisheries Genetics Laboratory<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#2E74B5">Environment Centre Wales<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#2E74B5">Bangor Unversity<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#2E74B5">LL57 2UW<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#2E74B5"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#2E74B5">Email: <a href="mailto:osue37@bangor.ac.uk">
<span style="color:#0563C1">osue37@bangor.ac.uk</span></a><o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#2E74B5">Skype: fairweathr<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#2E74B5">Twitter: @FairweathR<o:p></o:p></span></p>
</div>
<p class="MsoNormal"><span style="color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<div>
<div style="border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0cm 0cm 0cm">
<p class="MsoNormal"><b><span lang="EN-US">From:</span></b><span lang="EN-US"> Robert Fairweather
<br>
<b>Sent:</b> 09 October 2015 15:02<br>
<b>To:</b> 'Jombart, Thibaut' <t.jombart@imperial.ac.uk><br>
<b>Subject:</b> RE: Converting between adegenet and genetics<o:p></o:p></span></p>
</div>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span style="color:#1F497D;mso-fareast-language:EN-US">Dear Thibaut,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D;mso-fareast-language:EN-US">Many thanks for your response. Specifically I am trying to convert my genind object into genepop format so that I can use genetics to export it as a .gen file in said format. I have
been getting the impression that support for genetics is waning across the board, and so am looking into alternative packages that may be able to save genepops and which adegenet can export to. Please do let me know if you know any. My data is co-dominant
SNP data, originally imported into adegenet as a .gen file.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D;mso-fareast-language:EN-US">Cheers,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D;mso-fareast-language:EN-US">Robert<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<div>
<div style="border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0cm 0cm 0cm">
<p class="MsoNormal"><b><span lang="EN-US">From:</span></b><span lang="EN-US"> Jombart, Thibaut [<a href="mailto:t.jombart@imperial.ac.uk">mailto:t.jombart@imperial.ac.uk</a>]
<br>
<b>Sent:</b> 09 October 2015 14:56<br>
<b>To:</b> Robert Fairweather <<a href="mailto:osue37@bangor.ac.uk">osue37@bangor.ac.uk</a>>;
<a href="mailto:adegenet-forum@lists.r-forge.r-project.org">adegenet-forum@lists.r-forge.r-project.org</a><br>
<b>Subject:</b> RE: Converting between adegenet and genetics<o:p></o:p></span></p>
</div>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Tahoma",sans-serif;color:black">Dear Robert,
<o:p></o:p></span></p>
<div>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Tahoma",sans-serif;color:black"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Tahoma",sans-serif;color:black">as of version 2.0.0, adegenet is no longer interfaced with the package genetics, but is meant to work with a number of others: hierfstat, pegas, poppr, ape, etc.
I believe most functionalities implemented in genetics are implemented elsewhere, but please let me know if something is missing.<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Tahoma",sans-serif;color:black"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Tahoma",sans-serif;color:black">Cheers<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Tahoma",sans-serif;color:black">Thibaut<o:p></o:p></span></p>
</div>
<div>
<div>
<div>
<div>
<div>
<p class="MsoNormal" style="margin-bottom:12.0pt"><span style="font-size:10.0pt;font-family:"Tahoma",sans-serif;color:black"> <o:p></o:p></span></p>
</div>
</div>
</div>
</div>
<div>
<div class="MsoNormal" align="center" style="text-align:center"><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black">
<hr size="2" width="100%" align="center">
</span></div>
<div id="divRpF494343">
<p class="MsoNormal" style="margin-bottom:12.0pt"><b><span style="font-size:10.0pt;font-family:"Tahoma",sans-serif;color:black">From:</span></b><span style="font-size:10.0pt;font-family:"Tahoma",sans-serif;color:black">
<a href="mailto:adegenet-forum-bounces@lists.r-forge.r-project.org">adegenet-forum-bounces@lists.r-forge.r-project.org</a> [adegenet-forum-bounces@lists.r-forge.r-project.org] on behalf of Robert Fairweather [osue37@bangor.ac.uk]<br>
<b>Sent:</b> 09 October 2015 14:46<br>
<b>To:</b> <a href="mailto:adegenet-forum@lists.r-forge.r-project.org">adegenet-forum@lists.r-forge.r-project.org</a><br>
<b>Subject:</b> [adegenet-forum] Converting between adegenet and genetics</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
<div>
<div>
<p class="MsoNormal"><span style="color:black">Dear Thibaut,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black">I am trying to export a genind object from adegenet to genetics package format so that I can use functions in that package not available in adegenet. The adegenet homepage suggests that this is possible, but I
cannot find anything in the instruction pdf detailing the appropriate function(s). An earlier post suggests the function genind2genotype, but this does not exist in the manual and cannot be found in the version of adegenet that I am using (2.0.0).<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black">How can I export my genind object into genetics?<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black">Best wishes,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black">Robert<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black"> <o:p></o:p></span></p>
</div>
<p><span style="color:black"> <o:p></o:p></span></p>
<table class="MsoNormalTable" border="0" cellspacing="0" cellpadding="0" width="100%" style="width:100.0%">
<tbody>
<tr>
<td valign="top" style="padding:11.25pt 0cm 11.25pt 0cm">
<p><strong>Rhif Elusen Gofrestredig 1141565 - Registered Charity No. 1141565</strong><o:p></o:p></p>
<p>Gall y neges e-bost hon, ac unrhyw atodiadau a anfonwyd gyda hi, gynnwys deunydd cyfrinachol ac wedi eu bwriadu i'w defnyddio'n unig gan y sawl y cawsant eu cyfeirio ato (atynt). Os ydych wedi derbyn y neges e-bost hon trwy gamgymeriad, rhowch wybod i'r
anfonwr ar unwaith a dilewch y neges. Os na fwriadwyd anfon y neges atoch chi, rhaid i chi beidio a defnyddio, cadw neu ddatgelu unrhyw wybodaeth a gynhwysir ynddi. Mae unrhyw farn neu safbwynt yn eiddo i'r sawl a'i hanfonodd yn unig ac nid yw o anghenraid
yn cynrychioli barn Prifysgol Bangor. Nid yw Prifysgol Bangor yn gwarantu bod y neges e-bost hon neu unrhyw atodiadau yn rhydd rhag firysau neu 100% yn ddiogel. Oni bai fod hyn wedi ei ddatgan yn uniongyrchol yn nhestun yr e-bost, nid bwriad y neges e-bost
hon yw ffurfio contract rhwymol - mae rhestr o lofnodwyr awdurdodedig ar gael o Swyddfa Cyllid Prifysgol Bangor.<o:p></o:p></p>
<p>This email and any attachments may contain confidential material and is solely for the use of the intended recipient(s). If you have received this email in error, please notify the sender immediately and delete this email. If you are not the intended recipient(s),
you must not use, retain or disclose any information contained in this email. Any views or opinions are solely those of the sender and do not necessarily represent those of Bangor University. Bangor University does not guarantee that this email or any attachments
are free from viruses or 100% secure. Unless expressly stated in the body of the text of the email, this email is not intended to form a binding contract - a list of authorised signatories is available from the Bangor University Finance Office.<o:p></o:p></p>
</td>
</tr>
</tbody>
</table>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Times New Roman",serif"><o:p> </o:p></span></p>
</div>
</div>
</div>
</div>
</div>
<p> </p>
<table width="100%" border="0" cellpadding="0" cellspacing="0">
<tbody>
<tr>
<td valign="top" style="padding:15px 0;">
<p><strong>Rhif Elusen Gofrestredig 1141565 - Registered Charity No. 1141565</strong></p>
<p>Gall y neges e-bost hon, ac unrhyw atodiadau a anfonwyd gyda hi, gynnwys deunydd cyfrinachol ac wedi eu bwriadu i'w defnyddio'n unig gan y sawl y cawsant eu cyfeirio ato (atynt). Os ydych wedi derbyn y neges e-bost hon trwy gamgymeriad, rhowch wybod i'r
anfonwr ar unwaith a dilewch y neges. Os na fwriadwyd anfon y neges atoch chi, rhaid i chi beidio a defnyddio, cadw neu ddatgelu unrhyw wybodaeth a gynhwysir ynddi. Mae unrhyw farn neu safbwynt yn eiddo i'r sawl a'i hanfonodd yn unig ac nid yw o anghenraid
yn cynrychioli barn Prifysgol Bangor. Nid yw Prifysgol Bangor yn gwarantu bod y neges e-bost hon neu unrhyw atodiadau yn rhydd rhag firysau neu 100% yn ddiogel. Oni bai fod hyn wedi ei ddatgan yn uniongyrchol yn nhestun yr e-bost, nid bwriad y neges e-bost
hon yw ffurfio contract rhwymol - mae rhestr o lofnodwyr awdurdodedig ar gael o Swyddfa Cyllid Prifysgol Bangor.</p>
<p>This email and any attachments may contain confidential material and is solely for the use of the intended recipient(s). If you have received this email in error, please notify the sender immediately and delete this email. If you are not the intended recipient(s),
you must not use, retain or disclose any information contained in this email. Any views or opinions are solely those of the sender and do not necessarily represent those of Bangor University. Bangor University does not guarantee that this email or any attachments
are free from viruses or 100% secure. Unless expressly stated in the body of the text of the email, this email is not intended to form a binding contract - a list of authorised signatories is available from the Bangor University Finance Office.</p>
</td>
</tr>
</tbody>
</table>
</body>
</html>