<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="">You need to view the output the programs produce, not the HMM. You can Run them through MAKER and then view the GFF3 files produced<div class=""><br class=""></div><div class="">Here is a MAKER tutorial where this is done that you can follow along if you wish —> <a href="http://gmod.org/wiki/MAKER_Tutorial_2013#Training_ab_initio_Gene_Predictors" class="">http://gmod.org/wiki/MAKER_Tutorial_2013#Training_ab_initio_Gene_Predictors</a></div><div class=""><br class=""></div><div class="">For Augustus training there are a number of threads related to how to do that on the MAKER mailing list archives — <a href="https://groups.google.com/forum/#!searchin/maker-devel/augustus" class="">https://groups.google.com/forum/#!searchin/maker-devel/augustus</a></div><div class="">Also other resources online —> <a href="http://www.molecularevolution.org/molevolfiles/exercises/augustus/training.html" class="">http://www.molecularevolution.org/molevolfiles/exercises/augustus/training.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><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Feb 11, 2016, at 5:18 PM, hcma <<a href="mailto:hcma@uci.edu" class="">hcma@uci.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">Hi Carson,</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">I have downloaded Apollo and what format of the SNAP and Augustus models does Apollo take? Do i need to reformat the SNAP.hmm and which output of Augustus to use if I train Augustus manually?</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">Thanks again for your time.</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">Best Regards</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">Karen</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">On 2016-02-05 06:36, Carson Holt wrote:</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><blockquote type="cite" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">Hi Karen,<br class="">There are many ways to train Augustus. I prefer to identify gene<br class="">models in MAKER (GFF3) and use those to train both SNAP and Augustus.<br class="">Here is a previous post on the topic —><br class=""><a href="https://groups.google.com/forum/#!searchin/maker-devel/augustus/maker-devel/FWMSTdqWQqI/lC3miQtiCpwJ" class="">https://groups.google.com/forum/#!searchin/maker-devel/augustus/maker-devel/FWMSTdqWQqI/lC3miQtiCpwJ</a><br class="">[1]<br class="">In the end you need to look at the SNAP and Augustus models together<br class="">with evidence alignments in a genome browser (like desktop Apollo).<br class="">When everything is trained well, both SNAP and Augustus models will<br class="">look like each other and both seem to look like the evidence<br class="">alignments.<br class="">Thanks,<br class="">Carson<br class=""><blockquote type="cite" class="">On Feb 4, 2016, at 5:52 PM, hcma <<a href="mailto:hcma@uci.edu" class="">hcma@uci.edu</a>> wrote:<br class="">Hi,<br class="">I have a genome sequence and Trinity assembly for a new species and<br class="">I am wondering what are the best steps to take when using MAKER?<br class="">1. I used the genome sequence and all assembled Trinity sequence to<br class="">do first run of MAKER in order to generate training set for SNAP and<br class="">Augustus.<br class="">In maker_opts.ctl:<br class="">genome=all-chromosome-r1.04.fasta<br class="">est=Trinity.fasta<br class="">est2genome=1<br class="">2. Train SNAP<br class="">3. Train Augustus<br class="">When i train Augustus, i only supply genome and protein file, should<br class="">i also supply the trinity file here?<br class="">4. what's the best parameter to use when running MAKER the second<br class="">time for obtaining the final annotation? I would prefer not to use<br class="">any external protein data.<br class="">genome=all-chromosome-r1.04.fasta<br class="">est=Trinity.fasta<br class="">est2genome=0<br class="">SNAP<br class="">Augustus<br class="">Thanks.<br class="">Best Regards<br class="">KAren<br class=""></blockquote>Links:<br class="">------<br class="">[1]<br class=""><a href="https://groups.google.com/forum/#!searchin/maker-devel/augustus/maker-devel/FWMSTdqWQqI/lC3miQtiCpwJ" class="">https://groups.google.com/forum/#!searchin/maker-devel/augustus/maker-devel/FWMSTdqWQqI/lC3miQtiCpwJ</a></blockquote></div></blockquote></div><br class=""></div></body></html>