First, we are happy to announc=
e that this release is the first announced version of a mothur-based approa=
ch to open and closed reference clustering that doesn't suffer from the=
same problems found with other algorithms. This can be achieved using the =
cluster.fit function. =
You can read more about it in a paper we recently had accepted in mSphere. =
A preprint version of the paper can be found .org/content/10.1101/2021.11.09.468000v1.full.pdf">here while we wait f=
or the official publication.

Second, over the past=
few months we=E2=80=99ve incorporated a number of significant improvements=
to mothur to make it easier to work with by consolidating commands. For ex=
ample, we have included the ability to use screen.seqs arguments within mak=
e.contigs. This means that you can now do "make.contigs(file=3Dstabili=
ty.files, maxambig=3D0, maxlength=3D275, maxhomop=3D8)" as a single co=
mmand rather than two commands. We are also trying to phase out the names a=
nd groups files=C2=A0 in place of a count file since they add confusion and=
extra steps. Another notable change is that, by default, the chimera comma=
nds will remove the sequences from the fasta file so that you no longer nee=
d to use the subsequent remove.seqs command.=C2=A0

Third, if you've been to one of my workshops you know that=
the hardest step can often be getting to the correct place using the comma=
nd prompt. Now, if you double click on the mothur executable it *should* st=
art mothur in the directory where the executable was found. We are calling =
this the 'mothurhome' argument

Fourth, we =
found a small bug in pcr.seqs that inadvertently=C2=A0removed the first bas=
e from the outputted sequences. You may notice a one-base difference in the=
start/end coordinate positions between versions.

=
There's a few other things you might be interested in. Go ahead and che=
ck them out over at the=C2=A0leases/tag/v.1.47.0">release page when you get your new version of moth=
ur ;)

Finally, I continue =
to put a lot of effort into developing educational content that should be o=
f interest to mothur users. I am posting two videos each week to YouTube th=
at often uses mothur-based files as input to work within R. You can find th=
ese at the=C2=A0get=3D"_blank">Riffomonas YouTube channel. If you are interested in upc=
oming R and mothur workshops be sure to check out the schedule for=C2=A0href=3D"https://riffomonas.org/workshops/" target=3D"_blank">virtual worksh=
ops; I'll be teaching an R workshop in a couple of weeks! If you=
9;re looking for more updates on Riffomonas and resources for strengthening=
your R skills, I have a=C2=A0 target=3D"_blank">free weekly newsletter=C2=A0that you can subscribe t=
o. I've been encouraged by the positive feedback I've received from=
the content on Riffomonas - let me know if there's anything you'd =
like me to be sure to cover.

Enjoy the new releas=
e!
Pat