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MESSAGE
DATE 2022-01-26
FROM From: "Pat Schloss"
SUBJECT Subject: [Hangout - NYLXS] [mothur] mothur v.1.47.0 release
From hangout-bounces-at-nylxs.com Wed Jan 26 17:31:02 2022
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From: "Pat Schloss"
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Subject: [Hangout - NYLXS] [mothur] mothur v.1.47.0 release
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Hello mothur users!

We are happy to announce the release of mothur v.1.47.0
. There are a few
significant thigns to report with this release...

First, we are happy to announce that this release is the first announced
version of a mothur-based approach 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 here

while we wait for the official publication.

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

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 command prompt. Now, if
you double click on the mothur executable it *should* start 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 removed the
first base 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 check
them out over at the release page
when you get your
new version of mothur ;)

Finally, I continue to put a lot of effort into developing educational
content that should be of interest to mothur users. I am posting two videos
each week to YouTube that often uses mothur-based files as input to work
within R. You can find these at the Riffomonas YouTube channel
. If you are interested in
upcoming R and mothur workshops be sure to check out the schedule for virtu=
al
workshops ; I'll be teaching an R
workshop in a couple of weeks! If you're looking for more updates on
Riffomonas and resources for strengthening your R skills, I have a free
weekly newsletter that you can
subscribe to. 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 release!
Pat


-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-
Groups.io Links: You receive all messages sent to this group.
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Mute This Topic: https://groups.io/mt/88705793/321522
Group Owner: mothur+owner-at-groups.io
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--000000000000d192f005d681c8c6
Content-Type: text/html; charset="UTF-8"
Content-Transfer-Encoding: quoted-printable

Hello=C2=A0mothu=
r
=C2=A0users!

We are happy to announce the release of=C2=A0pan class=3D"gmail-il">mothur=C2=A0hur/mothur/releases/tag/v.1.47.0">v.1.47.0<=
/a>. There are a few significant thigns to report with this release...>


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
r>
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




_._,_._,_

G=
roups.io Links:

You receive all messages sent to this group.

target=3D"_blank" href=3D"https://groups.io/g/mothur/message/36">View/Repl=
y Online (#36) | subject=3DRe:%20%5Bmothur%5D%20mothur%20v.1.47.0%20release">Reply To Group<=
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vate:%20Re:%20%5Bmothur%5D%20mothur%20v.1.47.0%20release">Reply To Sendera> | =
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le=3D"color:white;clear:both">_._,_._,_
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  57. 2022-01-18 Wietse Venema <wietse-at-porcupine.org> Re: [Hangout - NYLXS] Adding Additional domains and outgoing email
  58. 2022-01-12 Bill Cole <postfixlists-070913-at-billmail.scconsult.com> Re: [Hangout - NYLXS] Adding Additional domains and outgoing email
  59. 2022-01-18 Wietse Venema <wietse-at-porcupine.org> Re: [Hangout - NYLXS] Adding a second line to .forward,
  60. 2022-01-12 Bill Cole <postfixlists-070913-at-billmail.scconsult.com> Re: [Hangout - NYLXS] Adding Additional domains and outgoing email
  61. 2022-01-12 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Hangout - NYLXS] Adding Additional domains and outgoing email
  62. 2022-01-12 Wietse Venema <wietse-at-porcupine.org> Re: [Hangout - NYLXS] Adding Additional domains and outgoing email
  63. 2022-01-12 Wietse Venema <wietse-at-porcupine.org> Re: [Hangout - NYLXS] Adding Additional domains and outgoing email
  64. 2022-01-11 raf <postfix-at-raf.org> Re: [Hangout - NYLXS] Adding Additional domains and outgoing email
  65. 2022-01-11 Phil Biggs <mb170712-at-pjb.cc> Subject: [Hangout - NYLXS] Virtual users with postfix and dovecot
  66. 2022-01-11 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Hangout - NYLXS] Adding Additional domains and outgoing email
  67. 2022-01-18 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Hangout - NYLXS] Adding Additional domains and outgoing email
  68. 2022-01-18 Matus UHLAR - fantomas <uhlar-at-fantomas.sk> Re: [Hangout - NYLXS] Adding Additional domains and outgoing email
  69. 2022-01-18 Wietse Venema <wietse-at-porcupine.org> Re: [Hangout - NYLXS] Adding Additional domains and outgoing email
  70. 2022-01-18 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Hangout - NYLXS] Adding Additional domains and outgoing email
  71. 2022-01-18 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Hangout - NYLXS] Adding Additional domains and outgoing email
  72. 2022-01-18 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Hangout - NYLXS] Adding Additional domains and outgoing email
  73. 2022-01-18 Wietse Venema <wietse-at-porcupine.org> Re: [Hangout - NYLXS] Adding Additional domains and outgoing email
  74. 2022-01-18 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Hangout - NYLXS] Adding Additional domains and outgoing email
  75. 2022-01-18 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Hangout - NYLXS] Adding Additional domains and outgoing email
  76. 2022-01-18 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Hangout - NYLXS] Adding Additional domains and outgoing email
  77. 2022-01-18 Wietse Venema <wietse-at-porcupine.org> Re: [Hangout - NYLXS] Adding Additional domains and outgoing email
  78. 2022-01-11 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Hangout - NYLXS] Adding Additional domains and outgoing email
  79. 2022-01-12 Wietse Venema <wietse-at-porcupine.org> Re: [Hangout - NYLXS] Adding Additional domains and outgoing email
  80. 2022-01-11 Bill Cole <postfixlists-070913-at-billmail.scconsult.com> Re: [Hangout - NYLXS] Adding Additional domains and outgoing email
  81. 2022-01-11 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Hangout - NYLXS] Adding Additional domains and outgoing email
  82. 2022-01-18 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Hangout - NYLXS] Adding Additional domains and outgoing email
  83. 2022-01-18 Chris Green <cl-at-isbd.net> Re: [Hangout - NYLXS] Adding a second line to .forward,
  84. 2022-01-18 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Hangout - NYLXS] Adding Additional domains and outgoing email
  85. 2022-01-18 Wietse Venema <wietse-at-porcupine.org> Re: [Hangout - NYLXS] Adding Additional domains and outgoing email
  86. 2022-01-11 Phil Biggs <mb170712-at-pjb.cc> Subject: [Hangout - NYLXS] Virtual users with postfix and dovecot
  87. 2022-01-18 Wietse Venema <wietse-at-porcupine.org> Re: [Hangout - NYLXS] Adding Additional domains and outgoing email
  88. 2022-01-12 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Hangout - NYLXS] Adding Additional domains and outgoing email
  89. 2022-01-18 Wietse Venema <wietse-at-porcupine.org> Re: [Hangout - NYLXS] Adding a second line to .forward,
  90. 2022-01-12 Wietse Venema <wietse-at-porcupine.org> Re: [Hangout - NYLXS] Adding Additional domains and outgoing email
  91. 2022-01-11 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Hangout - NYLXS] Adding Additional domains and outgoing email
  92. 2022-01-12 Wietse Venema <wietse-at-porcupine.org> Re: [Hangout - NYLXS] Adding Additional domains and outgoing email
  93. 2022-01-11 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Hangout - NYLXS] Adding Additional domains and outgoing email
  94. 2022-01-06 Viktor Dukhovni <postfix-users-at-dukhovni.org> Re: [Hangout - NYLXS] Adding Additional domains and outgoing email
  95. 2022-01-11 raf <postfix-at-raf.org> Re: [Hangout - NYLXS] Adding Additional domains and outgoing email
  96. 2022-01-06 raf <postfix-at-raf.org> Re: [Hangout - NYLXS] Adding Additional domains and outgoing email
  97. 2022-01-05 raf <postfix-at-raf.org> Re: [Hangout - NYLXS] Adding Additional domains and outgoing email
  98. 2022-01-05 Viktor Dukhovni <postfix-users-at-dukhovni.org> Re: [Hangout - NYLXS] Adding Additional domains and outgoing email
  99. 2022-01-05 Viktor Dukhovni <postfix-users-at-dukhovni.org> Re: [Hangout - NYLXS] Adding Additional domains and outgoing email
  100. 2022-01-12 Bill Cole <postfixlists-070913-at-billmail.scconsult.com> Re: [Hangout - NYLXS] Adding Additional domains and outgoing email
  101. 2022-01-12 Bill Cole <postfixlists-070913-at-billmail.scconsult.com> Re: [Hangout - NYLXS] Adding Additional domains and outgoing email
  102. 2022-01-11 Bill Cole <postfixlists-070913-at-billmail.scconsult.com> Re: [Hangout - NYLXS] Adding Additional domains and outgoing email
  103. 2022-01-11 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Hangout - NYLXS] Adding Additional domains and outgoing email
  104. 2022-01-12 Wietse Venema <wietse-at-porcupine.org> Re: [Hangout - NYLXS] Adding Additional domains and outgoing email
  105. 2022-01-11 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Hangout - NYLXS] Adding Additional domains and outgoing email
  106. 2022-01-05 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Hangout - NYLXS] Adding Additional domains and outgoing email
  107. 2022-01-18 Matus UHLAR - fantomas <uhlar-at-fantomas.sk> Re: [Hangout - NYLXS] Adding Additional domains and outgoing email
  108. 2022-01-18 From: "Joe Acquisto-j4" <joea-at-j4computers.com> Re: [Hangout - NYLXS] SASL questions
  109. 2022-01-18 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Hangout - NYLXS] Adding Additional domains and outgoing email
  110. 2022-01-18 Paul Robert Marino <prmarino1-at-gmail.com> Subject: [Hangout - NYLXS] Fwd: SASL questions
  111. 2022-01-18 Ruben Safir <mrbrklyn-at-panix.com> Subject: [Hangout - NYLXS] (fwd) de Blasio ruined New York City
  112. 2022-01-18 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Hangout - NYLXS] Check this out. It doesn
  113. 2022-01-18 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Hangout - NYLXS] Chofitz Chaim Auction needs some help...
  114. 2022-01-18 From: "Free Software Foundation" <info-at-fsf.org> Subject: [Hangout - NYLXS] FSF expands process for associate members to
  115. 2022-01-19 Rick Moen <rick-at-linuxmafia.com> Re: [Hangout - NYLXS] Check this out. It doesn
  116. 2022-01-20 aviva <aviva-at-gmx.us> Re: [Hangout - NYLXS] Check this out. It doesn
  117. 2022-01-20 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Hangout - NYLXS] Check this out. It doesn
  118. 2022-01-19 From: "Free Software Foundation" <info-at-fsf.org> Subject: [Hangout - NYLXS] New year,
  119. 2022-01-24 G?bor Szab? <gabor-at-szabgab.com> Subject: [Hangout - NYLXS] [Perlweekly] #548 - Perl Books Collection
  120. 2022-01-25 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Hangout - NYLXS] The suppresion of desenting scientific opinions
  121. 2022-01-26 From: "Pat Schloss" <pschloss-at-umich.edu> Subject: [Hangout - NYLXS] [mothur] mothur v.1.47.0 release
  122. 2022-01-28 Ruben Safir <mrbrklyn-at-panix.com> Subject: [Hangout - NYLXS] security and Free Software in the WSJ - eh
  123. 2022-01-29 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Hangout - NYLXS] New Zealand Lockdown
  124. 2022-01-30 Steve Hay <stevehay-at-apache.org> Subject: [Hangout - NYLXS] [ANNOUNCE] mod_perl-2.0.12

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