<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=utf-8">
<meta name="Generator" content="Microsoft Word 14 (filtered medium)">
<style><!--
/* Font Definitions */
@font-face
{font-family:Wingdings;
panose-1:5 0 0 0 0 0 0 0 0 0;}
@font-face
{font-family:Wingdings;
panose-1:5 0 0 0 0 0 0 0 0 0;}
@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:12.0pt;
font-family:"Times New Roman","serif";}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:purple;
text-decoration:underline;}
span.EmailStyle17
{mso-style-type:personal-reply;
font-family:"Calibri","sans-serif";
color:#1F497D;}
.MsoChpDefault
{mso-style-type:export-only;
mso-fareast-language:EN-US;}
@page WordSection1
{size:612.0pt 792.0pt;
margin:70.85pt 70.85pt 70.85pt 70.85pt;}
div.WordSection1
{page:WordSection1;}
/* List Definitions */
@list l0
{mso-list-id:294141486;
mso-list-template-ids:1277466466;}
@list l0:level1
{mso-level-number-format:bullet;
mso-level-text:;
mso-level-tab-stop:36.0pt;
mso-level-number-position:left;
text-indent:-18.0pt;
mso-ansi-font-size:10.0pt;
font-family:Symbol;}
@list l0:level2
{mso-level-number-format:bullet;
mso-level-text:o;
mso-level-tab-stop:72.0pt;
mso-level-number-position:left;
text-indent:-18.0pt;
mso-ansi-font-size:10.0pt;
font-family:"Courier New";
mso-bidi-font-family:"Times New Roman";}
@list l0:level3
{mso-level-number-format:bullet;
mso-level-text:;
mso-level-tab-stop:108.0pt;
mso-level-number-position:left;
text-indent:-18.0pt;
mso-ansi-font-size:10.0pt;
font-family:Wingdings;}
@list l0:level4
{mso-level-number-format:bullet;
mso-level-text:;
mso-level-tab-stop:144.0pt;
mso-level-number-position:left;
text-indent:-18.0pt;
mso-ansi-font-size:10.0pt;
font-family:Wingdings;}
@list l0:level5
{mso-level-number-format:bullet;
mso-level-text:;
mso-level-tab-stop:180.0pt;
mso-level-number-position:left;
text-indent:-18.0pt;
mso-ansi-font-size:10.0pt;
font-family:Wingdings;}
@list l0:level6
{mso-level-number-format:bullet;
mso-level-text:;
mso-level-tab-stop:216.0pt;
mso-level-number-position:left;
text-indent:-18.0pt;
mso-ansi-font-size:10.0pt;
font-family:Wingdings;}
@list l0:level7
{mso-level-number-format:bullet;
mso-level-text:;
mso-level-tab-stop:252.0pt;
mso-level-number-position:left;
text-indent:-18.0pt;
mso-ansi-font-size:10.0pt;
font-family:Wingdings;}
@list l0:level8
{mso-level-number-format:bullet;
mso-level-text:;
mso-level-tab-stop:288.0pt;
mso-level-number-position:left;
text-indent:-18.0pt;
mso-ansi-font-size:10.0pt;
font-family:Wingdings;}
@list l0:level9
{mso-level-number-format:bullet;
mso-level-text:;
mso-level-tab-stop:324.0pt;
mso-level-number-position:left;
text-indent:-18.0pt;
mso-ansi-font-size:10.0pt;
font-family:Wingdings;}
@list l1
{mso-list-id:1097865067;
mso-list-template-ids:589595560;}
@list l1:level1
{mso-level-number-format:bullet;
mso-level-text:;
mso-level-tab-stop:36.0pt;
mso-level-number-position:left;
text-indent:-18.0pt;
mso-ansi-font-size:10.0pt;
font-family:Symbol;}
@list l1:level2
{mso-level-number-format:bullet;
mso-level-text:o;
mso-level-tab-stop:72.0pt;
mso-level-number-position:left;
text-indent:-18.0pt;
mso-ansi-font-size:10.0pt;
font-family:"Courier New";
mso-bidi-font-family:"Times New Roman";}
@list l1:level3
{mso-level-number-format:bullet;
mso-level-text:;
mso-level-tab-stop:108.0pt;
mso-level-number-position:left;
text-indent:-18.0pt;
mso-ansi-font-size:10.0pt;
font-family:Wingdings;}
@list l1:level4
{mso-level-number-format:bullet;
mso-level-text:;
mso-level-tab-stop:144.0pt;
mso-level-number-position:left;
text-indent:-18.0pt;
mso-ansi-font-size:10.0pt;
font-family:Wingdings;}
@list l1:level5
{mso-level-number-format:bullet;
mso-level-text:;
mso-level-tab-stop:180.0pt;
mso-level-number-position:left;
text-indent:-18.0pt;
mso-ansi-font-size:10.0pt;
font-family:Wingdings;}
@list l1:level6
{mso-level-number-format:bullet;
mso-level-text:;
mso-level-tab-stop:216.0pt;
mso-level-number-position:left;
text-indent:-18.0pt;
mso-ansi-font-size:10.0pt;
font-family:Wingdings;}
@list l1:level7
{mso-level-number-format:bullet;
mso-level-text:;
mso-level-tab-stop:252.0pt;
mso-level-number-position:left;
text-indent:-18.0pt;
mso-ansi-font-size:10.0pt;
font-family:Wingdings;}
@list l1:level8
{mso-level-number-format:bullet;
mso-level-text:;
mso-level-tab-stop:288.0pt;
mso-level-number-position:left;
text-indent:-18.0pt;
mso-ansi-font-size:10.0pt;
font-family:Wingdings;}
@list l1:level9
{mso-level-number-format:bullet;
mso-level-text:;
mso-level-tab-stop:324.0pt;
mso-level-number-position:left;
text-indent:-18.0pt;
mso-ansi-font-size:10.0pt;
font-family:Wingdings;}
ol
{margin-bottom:0cm;}
ul
{margin-bottom:0cm;}
--></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="blue" vlink="purple">
<div class="WordSection1">
<div>
<div>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Calibri","sans-serif";color:#376092;mso-style-textfill-fill-color:#376092;mso-style-textfill-fill-alpha:100.0%">Dear Ensembl Developer Team,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Calibri","sans-serif";color:#376092;mso-style-textfill-fill-color:#376092;mso-style-textfill-fill-alpha:100.0%"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Calibri","sans-serif";color:#376092;mso-style-textfill-fill-color:#376092;mso-style-textfill-fill-alpha:100.0%">My name is Christian Groß and I am a researcher at TU Delft, the Netherlands.
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Calibri","sans-serif";color:#376092;mso-style-textfill-fill-color:#376092;mso-style-textfill-fill-alpha:100.0%"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Calibri","sans-serif";color:#376092;mso-style-textfill-fill-color:#376092;mso-style-textfill-fill-alpha:100.0%">I am currently trying to compute PhyloP & PhastCon scores (from the PHAST Package) for some of your
alignments (</span><span style="font-family:"Calibri","sans-serif";color:#376092;mso-style-textfill-fill-color:#376092;mso-style-textfill-fill-alpha:100.0%">21 eutherian mammals EPO, 53 eutherian mammals EPO_LOW_COVERAGE, 4 sauropsids EPO, 7 sauropsids EPO_LOW_COVERAGE).
To utilize PhyloP and PhastCon I need model files created by phyloFit (another program from the PHAST Package). These model files contain a substitution rate matrix, a tree with branch lengths and estimates of nucleotide equilibrium frequencies.
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Calibri","sans-serif";color:#376092;mso-style-textfill-fill-color:#376092;mso-style-textfill-fill-alpha:100.0%">On your website (<a href="https://www.ensembl.org/info/genome/compara/index.html#species_tree"><span style="color:#0000BF;mso-style-textfill-fill-color:#0000BF;mso-style-textfill-fill-alpha:100.0%">https://www.ensembl.org/info/genome/compara/index.html#species_tree</span></a></span><span style="font-family:"Calibri","sans-serif";color:#17375E;mso-style-textfill-fill-color:#17375E;mso-style-textfill-fill-alpha:100.0%">)
below “Species tree” it is mentioned that you ran phyloFit to compute branch lengths to be able to compute constrained regions via Gerp. Besides of the species trees with branch lengths, I have not been successful in finding any other data generated by phyloFit
via ftp or API. Is it possible to provide the .mod files generated by phyloFit or any log file which gives information about the set parameters?
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Calibri","sans-serif";color:#17375E;mso-style-textfill-fill-color:#17375E;mso-style-textfill-fill-alpha:100.0%"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Calibri","sans-serif";color:#17375E;mso-style-textfill-fill-color:#17375E;mso-style-textfill-fill-alpha:100.0%">If you could help me in this matter you would help me a great deal.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Calibri","sans-serif";color:#17375E;mso-style-textfill-fill-color:#17375E;mso-style-textfill-fill-alpha:100.0%"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Calibri","sans-serif";color:#17375E;mso-style-textfill-fill-color:#17375E;mso-style-textfill-fill-alpha:100.0%">Best regards,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Calibri","sans-serif";color:#17375E;mso-style-textfill-fill-color:#17375E;mso-style-textfill-fill-alpha:100.0%"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Calibri","sans-serif";color:#17375E;mso-style-textfill-fill-color:#17375E;mso-style-textfill-fill-alpha:100.0%">Christian
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Calibri","sans-serif";color:#17375E;mso-style-textfill-fill-color:#17375E;mso-style-textfill-fill-alpha:100.0%"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
</div>
</div>
</div>
</body>
</html>