Test suite failures with latest version of Blast

[tillea]

Hello,
after the Debian package that is creating the latest Blast from ncbi-blast+ was upgraded to version 2.5.0 the pynast test suite shows some failures. You can find detailed information in the Debian bug tracking system.
Please feel free to ask for any details if the issue is not clear.
Kind regards, Andreas.

[tillea]

Hi,
upstream of ncbi-blast+ has provided a patch you can take over from the Debian packaging.
Kind regards, Andreas.

[gregcaporaso]

Hi @tillea, PyNAST has never support BLAST+, rather only legacy BLAST, and I'm in the process of trying to phase it out in favor of better tools for alignment. Do you have an idea of how many users it has from this distribution? If not many, it might make more sense for you to drop support for it as I'm essentially hoping to discontinue this project (though I haven't officially decided to do that yet).

[tillea]

On Thu, Dec 22, 2016 at 09:52:57AM -0800, Greg Caporaso wrote: Hi @tillea, PyNAST has never support BLAST+, rather only legacy BLAST,

Well, it seems with the provided patch it could work.

and I'm in the process of trying to phase it out in favor of better tools for alignment. Do you have an idea of how many users it has from this distribution?

In Debian we have so called popularity contest that users can switch on voluntarily - so the numbers are probably lower than the real usage. We also do not have numbers of Debian derivatives like Ubuntu and others. Here you can see a graph of the popcon numbers: https://qa.debian.org/popcon.php?package=pynast The most important number of the current usage is vote (=67) which is the number of people who use this package regularly (not just hanging around unused on the hard disk).

If not many, it might make more sense for you to drop support for it as I'm essentially hoping to discontinue this project (though I haven't officially decided to do that yet).

When comparing with other packages maintained by Debian Med this would have some bad influence on the workflow of several users. Kind regards Andreas.

…

-- http://fam-tille.de

[colinbrislawn]

Perhaps this is off topic or perhaps too soon to ask, but I'm curious what's next for NAST alignments if this program is discontinued. Do you also think that de novo alignments are more useful or are you hoping to refactor the functionality of NAST into a qiime2 plugin?

Thank you for your feedback, Greg.

PS For my own notes, here are two modern MSA programs:
HAlign: (fast centre star algorithm. vsearch implements something like this)
Infernal: uses structure of RNA. Used for greengenes.