<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">The MAKER-P fork was merged back into standard MAKER with version 2.29 (roughly 3 years ago - a separate download no longer exists). This is because MAKER-P’s functionality is almost entirely in accessory scripts and written protocols. The …/maker/bin/maker called by both MAKER2 and MAKER-P is actually the same script. So no need to rerun, because if you are using version 2.29 or later, you already ran it.<br class=""><div class=""><br class=""></div><div class="">Pseudogene calling is therefore handled by accessory scripts and protocols you can find here —> <a href="http://shiulab.plantbiology.msu.edu/wiki/index.php/Protocol:Pseudogene" class="">http://shiulab.plantbiology.msu.edu/wiki/index.php/Protocol:Pseudogene</a></div><div class=""><br class=""></div><div class="">The other MAKER-P protocols can be found here —> <a href="http://www.yandell-lab.org/software/maker-p.html" class="">http://www.yandell-lab.org/software/maker-p.html</a> </div><div class=""><br class=""></div><div class="">--Carson</div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Jul 31, 2017, at 5:02 PM, Quanwei Zhang <<a href="mailto:qwzhang0601@gmail.com" class="">qwzhang0601@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div class=""><div class=""><div class=""><div class=""><div class=""><div class="">Hello:<br class=""><br class=""></div>We used Maker2 to annotate a new rodent genome. By using the annotated genes we did gene family expansion analysis, and found several gene families under expansion in the new rodent genome. But we want to check whether some annotated genes are Pseudogenes, which lead to the expansion. Do you have any suggestions on this?<br class=""><br class=""></div>We found the Maker-P can annotate Pseudogene, but we are not sure whether it is worth to repeat our annotation with Maker-P. Besides, we are not sure whether the default parameters of Maker-P are good for a rodent species. What's more, in my understanding the Maker-P will identify Pseudogenes in the intergenic spaces (which I think the annotated coding genes will be not be tested and checked).<br class=""><br class=""></div>Do you have any suggestions to solve our problem? We do not want to identify Pseudogene on the genome wide, but only want to check those genes showing expansion (to make sure all those gene copies really function).<br class=""><br class=""></div>Many thanks<br class=""><br class=""></div>Best<br class=""></div>Quanwei<br class=""><div class=""><div class=""><div class=""><div class=""><br class=""></div></div></div></div></div>
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