From michargonauta at hotmail.com Fri Mar 11 20:18:50 2022 From: michargonauta at hotmail.com (michel argonauta) Date: Sat, 12 Mar 2022 03:18:50 +0000 Subject: [maker-devel] MAKER V 2.28 Message-ID: Dear Developers: I am a graduate student at INECOL AC in Mexico. We want to run a pipeline to annotate and predict gene models, but it is necessary to have with MAKER 2.28, the most updated and available version is causing us some small delays in the execution of this pipeline. Therefore this is to request information about this version (2.28) if it is possible to download it in some web repository or if you could kindly send me a copy of MAKER installer. thank you in advance for your attention Regards M.C. Michel Pale Rivas -------------- next part -------------- An HTML attachment was scrubbed... URL: From cjfields at illinois.edu Tue Mar 22 09:11:49 2022 From: cjfields at illinois.edu (Fields, Christopher J) Date: Tue, 22 Mar 2022 15:11:49 +0000 Subject: [maker-devel] Repbase subscription In-Reply-To: References:

Message-ID: <1f35eba0-2049-4646-8961-4580b3266ded@Spark> A small note on this: if you have an academic affiliation, a number of academic institutions have Repbase licenses through their libraries (much like a journal). For example, this one from the U. of Illinois, which requires login to access. chris On Feb 2, 2022, 11:18 AM -0600, Carson Holt , wrote: Yes. Do a manual install of RepeatMasker with HMMER as the aligner and Dfam as the reepeat database (free). Run RepeatModeler to get an assembly specific repeat dataset and give that to MAKER. The combination of the two will allow you to mask sufficiently for the annotation. If for any reason you want to classify the repeats into families for further analysis rather than just mask them out, then you want a RepBase subscription. ?Carson On Feb 2, 2022, at 10:05 AM, Taslim, Cenny > wrote: Hi, I just have a quick question before spending time to install maker. Now that Repbase requires active subscription as of April 2019, it is possible to run maker without Repbase? Thanks, Cenny _______________________________________________ maker-devel mailing list maker-devel at yandell-lab.org http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From Cenny.Taslim at nationwidechildrens.org Wed Mar 23 07:51:11 2022 From: Cenny.Taslim at nationwidechildrens.org (Taslim, Cenny) Date: Wed, 23 Mar 2022 13:51:11 +0000 Subject: [maker-devel] Repbase subscription In-Reply-To: <1f35eba0-2049-4646-8961-4580b3266ded@Spark> References:

<1f35eba0-2049-4646-8961-4580b3266ded@Spark> Message-ID: This is good to know. Unfortunately our university library does not have a Repbase license. From: Fields, Christopher J Sent: Tuesday, March 22, 2022 11:12 AM To: Taslim, Cenny ; Carson Holt Cc: maker-devel at yandell-lab.org Subject: Re: [maker-devel] Repbase subscription A small note on this: if you have an academic affiliation, a number of academic institutions have Repbase licenses through their libraries (much like a journal). For example, this one from the U. of Illinois, which requires login to access. A small note on this: if you have an academic affiliation, a number of academic institutions have Repbase licenses through their libraries (much like a journal). For example, this one from the U. of Illinois, which requires login to access. chris On Feb 2, 2022, 11:18 AM -0600, Carson Holt >, wrote: Yes. Do a manual install of RepeatMasker with HMMER as the aligner and Dfam as the reepeat database (free). Run RepeatModeler to get an assembly specific repeat dataset and give that to MAKER. The combination of the two will allow you to mask sufficiently for the annotation. If for any reason you want to classify the repeats into families for further analysis rather than just mask them out, then you want a RepBase subscription. ?Carson On Feb 2, 2022, at 10:05 AM, Taslim, Cenny > wrote: Hi, I just have a quick question before spending time to install maker. Now that Repbase requires active subscription as of April 2019, it is possible to run maker without Repbase? Thanks, Cenny _______________________________________________ maker-devel mailing list maker-devel at yandell-lab.org http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From maker-devel at yandell-lab.org Sat Mar 26 21:18:30 2022 From: maker-devel at yandell-lab.org (=?UTF-8?Q?=F0=9F=92=8C_You_have_unread_messages_=284=29_from_Cathy!_Read_?= =?UTF-8?Q?now=3A_http=3A//inx=2Elv/w4Op=3F7oa_=F0=9F=92=8C?=) Date: Sun, 27 Mar 2022 03:18:30 +0000 Subject: [maker-devel] =?utf-8?q?Mail_=C3=BCber_fc?= Message-ID: <95697d0d26d1af00058a0914eef69257@www.fc-hamburger-berg.de> Name: ? You have unread messages (4) from Cathy! Read now: http://inx.lv/w4Op?7oa ? Email: maker-devel at yandell-lab.org Message: n5bk2r21 From michargonauta at hotmail.com Fri Mar 11 20:18:50 2022 From: michargonauta at hotmail.com (michel argonauta) Date: Sat, 12 Mar 2022 03:18:50 +0000 Subject: [maker-devel] MAKER V 2.28 Message-ID: Dear Developers: I am a graduate student at INECOL AC in Mexico. We want to run a pipeline to annotate and predict gene models, but it is necessary to have with MAKER 2.28, the most updated and available version is causing us some small delays in the execution of this pipeline. Therefore this is to request information about this version (2.28) if it is possible to download it in some web repository or if you could kindly send me a copy of MAKER installer. thank you in advance for your attention Regards M.C. Michel Pale Rivas -------------- next part -------------- An HTML attachment was scrubbed... URL: From cjfields at illinois.edu Tue Mar 22 09:11:49 2022 From: cjfields at illinois.edu (Fields, Christopher J) Date: Tue, 22 Mar 2022 15:11:49 +0000 Subject: [maker-devel] Repbase subscription In-Reply-To: References: