[maker-devel] Maker2 changelog and Maker3

[Carson Holt]

Also MAKER2 vs MAKER3.  Apart from EVM support, MAKER3 also has modified logic for est2genome and protein2genome that results in better forward mapping of old genes between assemblies and can use est_gff for UTR. MAKER2 only uses est_gff for predictor hints but not for UTR generation.

—Carson


> On Jun 2, 2020, at 12:57 AM, Xabier Vázquez-Campos <xvazquezc at gmail.com> wrote:
> 
> Hi Carson,
> 
> I was looking for some Maker-related stuff (not important what) and I realised that there was a new release in April for Maker 2 and Maker 3 was not in beta anymore.
> 
> We have been using Maker 2.31.9 in our cluster for a few years now and while the new (2.31.11) includes the most recent change (maker_functional_fasta and maker_functional_gff handle newer UniProt/Swiss-Prot format. Also fix for newer genemark command line structure) I can't find what changed in 2.31.10 nor a general changelog.
> By the way, do you know when (version) the genemark command line structure changed? What about the Uniprot format?
> 
> Also, is there any fundamental difference aside of the integration of EVM in Maker3 vs Maker2? I found this entry from 2 years ago and wanted to check if this is still the case.
> http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/2018-August/003279.html <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/2018-August/003279.html>
> 
> Thank you,
> Xabi
> 
> 
> PS: is there a way to receive notifications for new releases? I didn't notice anything in the mail list
> -- 
> Xabier Vázquez-Campos, PhD
> Research Associate
> NSW Systems Biology Initiative
> School of Biotechnology and Biomolecular Sciences
> The University of New South Wales
> Sydney NSW 2052 AUSTRALIA
> _______________________________________________
> 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: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20200821/2a3216b5/attachment-0002.html>