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Merge remote-tracking branch 'refs/remotes/origin/master'
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‎_wiki/clearcut.md‎

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@@ -55,12 +55,12 @@ The quiet parameter turns on silent operation mode, default=F.
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mothur > clearcut(fasta=abrecovery.align, DNA=T, quiet=t)
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### seed
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### rseed
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The seed parameter allows you to explicitly set the PRNG seed to a
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specific value.
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mothur > clearcut(fasta=abrecovery.align, DNA=t, seed=12345)
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mothur > clearcut(fasta=abrecovery.align, DNA=t, rseed=12345)
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### norandom
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### neighbor
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The neighbor parameter allows you to use traditional Neighbor-Joining
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algorithm, default=F.
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algorithm, default=T.
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mothur > clearcut(fasta=abrecovery.align, DNA=t, neighbor=t)
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mothur > clearcut(fasta=abrecovery.align, DNA=t, neighbor=f)
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### stdout
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‎_wiki/list_file.md‎

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@@ -12,33 +12,11 @@ of OTUs that have been formed. Subsequent columns contain the names of
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sequences within each OTU separated by a comma. At this time these are
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not sorted according to any rule.
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Sample output of 98\_sq\_phylip\_amazon.fn.list, which can be download
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in the AmazonData.zip file:
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unique 96  U68589  U68590  U68591  U68592  U68593  U68594  U68595  U68596  U68597  U68598  U68599  U68600
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   U68601  U68602  U68603  U68605  U68606  U68607  U68608  U68609  U68610  U68611  U68612  U68613  U68614
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   U68615  U68616  U68617  U68620,U68618   U68619  U68621  U68622  U68623  U68624  U68625  U68626  U68627
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   U68628  U68629  U68630  U68631  U68632  U68633  U68634  U68635  U68636  U68637  U68638  U68639  U68640
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   U68667,U68641   U68642  U68643  U68644  U68645  U68646  U68647  U68648  U68649  U68651  U68652  U68653
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   U68654  U68655  U68656  U68657  U68658  U68659  U68660  U68661  U68662  U68663  U68664  U68665  U68666
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   U68668  U68669  U68670  U68671  U68672  U68673  U68674  U68675  U68676  U68677  U68678  U68679  U68680
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   U68681  U68682  U68683  U68684  U68685  U68686  U68687  U68688  
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0.00   95  U68589  U68590  U68591  U68592  U68593  U68594  U68595  U68596  U68597  U68598  U68599  U68600
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   U68601  U68602  U68603  U68605  U68606  U68607  U68608  U68609  U68610  U68611  U68612  U68613  U68614
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   U68680,U68615   U68616  U68617  U68620,U68618   U68619  U68621  U68622  U68623  U68624  U68625  U68626
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   U68627  U68628  U68629  U68630  U68631  U68632  U68633  U68634  U68635  U68636  U68637  U68638  U68639
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   U68640  U68667,U68641   U68642  U68643  U68644  U68645  U68646  U68647  U68648  U68649  U68651  U68652
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   U68653  U68654  U68655  U68656  U68657  U68658  U68659  U68660  U68661  U68662  U68663  U68664  U68665
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   U68666  U68668  U68669  U68670  U68671  U68672  U68673  U68674  U68675  U68676  U68677  U68678  U68679
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   U68681  U68682  U68683  U68684  U68685  U68686  U68687  U68688  
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0.01   93  U68589  U68590  U68591  U68592  U68593  U68594  U68595  U68596  U68597  U68598  U68599  U68600
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   U68601  U68602  U68603  U68605  U68606  U68607  U68608  U68609  U68610  U68611  U68612  U68613  U68614
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   U68680,U68615   U68616  U68617  U68620,U68618   U68619  U68621  U68622  U68623  U68624  U68625  U68626
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   U68627  U68628  U68629  U68630  U68636,U68631   U68632  U68633  U68634  U68635  U68637  U68638  U68639
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   U68640  U68667,U68641   U68642  U68643  U68644  U68645  U68646  U68647  U68648  U68649  U68651  U68652
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   U68653  U68654  U68655  U68656  U68657  U68658  U68659  U68660  U68661  U68662  U68663  U68664
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   U68688,U68665   U68666  U68668  U68669  U68670  U68671  U68672  U68673  U68674  U68675  U68676  U68677
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   U68678  U68679  U68681  U68682  U68683  U68684  U68685  U68686  U68687  
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...
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Looking at the final.opti_mcc.list file from the [MiSeq_SOP](/wiki/MiSeq_SOP)
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label numOtus Otu001 Otu002 Otu003 Otu004 Otu005 Otu006 Otu007 Otu008 Otu009 Otu010 Otu011 ...
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0.03 531 M00967_43_000000000-A3JHG_1_1101_20262_22075,M00967_43_000000000-A3JHG_1_1113_28928_16770,
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M00967_43_000000000-A3JHG_1_1108_22866_20909,M00967_43_000000000-A3JHG_1_1112_18411_17052,M00967_43_000000000-A3JHG_1_1112_5981_8948,M00967_43_000000000-A3JHG_1_2108_7751_22068,M00967_43_000000000-A3JHG_1_2106_8030_23327,
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M00967_43_000000000-A3JHG_1_2114_4499_18914,M00967_43_000000000-A3JHG_1_1113_15967_2074,M00967_43_000000000-A3JHG_1_1109_24493_23253,M00967_43_000000000-A3JHG_1_2113_29656_14155,M00967_43_000000000-A3JHG_1_1111_20933_6700,
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M00967_43_000000000-A3JHG_1_2101_13320_3436,M00967_43_000000000-A3JHG_1_1107_13116_15821,M00967_43_000000000-A3JHG_1_1114_13556_18457,M00967_43_000000000-A3JHG_1_1109_7996_16802,M00967_43_000000000-A3JHG_1_2114_12634_10967,
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M00967_43_000000000-A3JHG_1_2106_18324_28644,...

‎_wiki/merge.files.md‎

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The **merge.files** command will concatenate
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multiple files and output the result to a new file. This command is
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useful for merging multiple fasta-formatted sequence files, 454 quality
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files, group files, name files, or anything else.
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files, group files, name files, or anything else except count_tables (see [merge.count](/wiki/merge.count/)).
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To run the **merge.files** command you need to provide the input files
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separated by hyphens as well as the name file that the contents of those

‎_wiki/miseq_sop.md‎

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[full
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dataset](https://mothur.org/MiSeqDevelopmentData/StabilityNoMetaG.tar)
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- [SILVA-based bacterial reference
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alignment](https://mothur.s3.us-east-2.amazonaws.com/wiki/silva.bacteria.zip)
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alignment (v102)](https://mothur.s3.us-east-2.amazonaws.com/wiki/silva.bacteria.zip)
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- [mothur-formatted version of the RDP training set
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(v.9)](https://mothur.s3.us-east-2.amazonaws.com/wiki/trainset9_032012.pds.zip)
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- 6/24/19 - Updated to reflect version 1.42.3 outputs.
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- 1/11/21 - Updates to reflect version 1.47.0 outputs.
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- 8/30/22 - Updates to reflect changes with 1.48.0 syntax
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- 8/30/22 - Updates to reflect changes with 1.48.0 syntax

‎_wiki/pcr.seqs.md‎

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The nomatch parameter allows you to decide what to do with sequences
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where the primer is not found. Default=reject, meaning remove from fasta
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file. if nomatch=keep, then do nothing to sequence.
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file. if nomatch=keep, then do nothing to sequence. Note: the nomatch parameter
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only used when running pcr.seqs with an oligos file.
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### keepprimer
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