# Integrating mothur with other programs **URL:** https://forum.mothur.org/c/integrating-mothur-with-other-programs/12.md?page=1 [Latest](https://forum.mothur.org/latest.md) · [Categories](https://forum.mothur.org/categories.md) **Page:** 2 --- ## [Use QIIME 2 files in mothur?](https://forum.mothur.org/t/use-qiime-2-files-in-mothur/19604)
**Author:** [@smreyes](https://forum.mothur.org/u/smreyes)\ **Replies:** 3\ **Last updated:** [November 27, 2018, 8:22pm UTC](https://forum.mothur.org/t/use-qiime-2-files-in-mothur/19604 "2018-11-27T20:22:38Z")
I’d really like to do some analyses in mothur that are not available in QIIME 2. However, I would like to use my OTU, taxonomy, and tree files that are already created in QIIME 2. Is there an easy way to do this? I trie… --- ## [Mothur and Python](https://forum.mothur.org/t/mothur-and-python/3446)
**Author:** [@campenr](https://forum.mothur.org/u/campenr)\ **Replies:** 0\ **Last updated:** [November 14, 2017, 7:39pm UTC](https://forum.mothur.org/t/mothur-and-python/3446 "2017-11-14T19:39:57Z")
Hello mothur community, In case it is of use to anyone else, I have built a Python (Python 3 only) wrapper for mothur called mothur-py. This wrapper was inspired by the ipython-mothurmagic plugin for the Jupyter (nee IP… --- ## [Get.oturep (changing fasta file header)](https://forum.mothur.org/t/get-oturep-changing-fasta-file-header/3401)
**Author:** [@lamab](https://forum.mothur.org/u/lamab)\ **Replies:** 2\ **Last updated:** [September 19, 2017, 5:26pm UTC](https://forum.mothur.org/t/get-oturep-changing-fasta-file-header/3401 "2017-09-19T17:26:32Z")
Dear colleagues, how are you doing? I would like to generate a tree of OTUs, in order to do some phylogenetic based analysis on R. To do this, I used the Get.oturep command. This command generated a fasta file with the … --- ## [make.lefse and galaxy](https://forum.mothur.org/t/make-lefse-and-galaxy/3373)
**Author:** [@Alex\_Thibodeau](https://forum.mothur.org/u/Alex_Thibodeau)\ **Replies:** 1\ **Last updated:** [August 31, 2017, 9:16pm UTC](https://forum.mothur.org/t/make-lefse-and-galaxy/3373 "2017-08-31T21:16:24Z")
Hello community I am using mothur 1.39.5 I used make.lefse to generate a lefse table (from my subsample.shared, design and constaxonomy files) that I uploaded to Galaxy (tab-delimited) to go through lefse. I really li… --- ## [Compute Canada](https://forum.mothur.org/t/compute-canada/3323)
**Author:** [@Alex\_Thibodeau](https://forum.mothur.org/u/Alex_Thibodeau)\ **Replies:** 8\ **Last updated:** [August 16, 2017, 7:56pm UTC](https://forum.mothur.org/t/compute-canada/3323 "2017-08-16T19:56:07Z")
Hello! Anybody ran Mothur on a Compute Canada machine? I have a question for how to set-up the number of processors that Mothur can use. In my .batch file, I have used set.current(processors=16) In my .sh file for SL… --- ## [MOTHUR vs QIIME x Tax4Fun -\> are all .biom equal?](https://forum.mothur.org/t/mothur-vs-qiime-x-tax4fun-are-all-biom-equal/2578)
**Author:** [@CECILETHION](https://forum.mothur.org/u/CECILETHION)\ **Replies:** 11\ **Last updated:** [June 29, 2017, 1:07pm UTC](https://forum.mothur.org/t/mothur-vs-qiime-x-tax4fun-are-all-biom-equal/2578 "2017-06-29T13:07:27Z")
Good afternoon, Please see at the end the different scripts I have implemented for trying to solve my problem, with # in (). I am currently working with a bacterial 16S Illumina sequencing dataset. I have cleaned, tri… --- ## [chimera.uchime running for ever](https://forum.mothur.org/t/chimera-uchime-running-for-ever/3250)
**Author:** [@jigyasa](https://forum.mothur.org/u/jigyasa)\ **Replies:** 1\ **Last updated:** [May 11, 2017, 12:10pm UTC](https://forum.mothur.org/t/chimera-uchime-running-for-ever/3250 "2017-05-11T12:10:46Z")
Hey guys! I am new to Microbiome analysis and Mothur. I was running the chimera.uchime code for my 96 samples (3,529,000 unique sequences) but the chimera.uchime has been running for almost 2 days. Does it usually take… --- ## [Make a DEB install package for MOTHUR](https://forum.mothur.org/t/make-a-deb-install-package-for-mothur/3201)
**Author:** [@cement\_head](https://forum.mothur.org/u/cement_head)\ **Replies:** 0\ **Last updated:** [April 6, 2017, 12:37pm UTC](https://forum.mothur.org/t/make-a-deb-install-package-for-mothur/3201 "2017-04-06T12:37:47Z")
Hi All, I’m interested in making a \<\*.deb\> install package for mothur and I was wondering if I could get some help from any of the Linux people to help with packaging. Regards, Andor --- ## [Mothur MPI make error](https://forum.mothur.org/t/mothur-mpi-make-error/3133)
**Author:** [@heyheyhey](https://forum.mothur.org/u/heyheyhey)\ **Replies:** 3\ **Last updated:** [February 21, 2017, 5:13pm UTC](https://forum.mothur.org/t/mothur-mpi-make-error/3133 "2017-02-21T17:13:14Z")
Hi, (Wasn’t sure what topic to put this under.) I’ve been trying to install MPI Mothur, but I can’t get past the ‘make’ command. \*\*Note: I can’t put anything into /usr/local (I don’t have permissions) So far I’ve… w… --- ## [Formating mothur data to Calypso](https://forum.mothur.org/t/formating-mothur-data-to-calypso/3132)
**Author:** [@nazen](https://forum.mothur.org/u/nazen)\ **Replies:** 0\ **Last updated:** [February 17, 2017, 10:18am UTC](https://forum.mothur.org/t/formating-mothur-data-to-calypso/3132 "2017-02-17T10:18:21Z")
Dear, all! I’m a new in 16S amplicon sequencing and I can not figure out how to convert or generate data from mothur into Calypso format in the manner of each OTU\\taxonomic group has a count of sequences. Could somebod… --- ## [Using PICRUSt with Mothur](https://forum.mothur.org/t/using-picrust-with-mothur/3113)
**Author:** [@stevn7](https://forum.mothur.org/u/stevn7)\ **Replies:** 2\ **Last updated:** [February 11, 2017, 12:34am UTC](https://forum.mothur.org/t/using-picrust-with-mothur/3113 "2017-02-11T00:34:20Z")
I want to use PICRUSt with some Illumina MiSeq 16S data that I’ve already processed on Mothur (using the MiSeq SOP), but I’m unclear about something. PICRUSt only works with Greengenes OTUs and I used the SILVA database … --- ## [NMDS biplot to show both samples and species using R](https://forum.mothur.org/t/nmds-biplot-to-show-both-samples-and-species-using-r/3053)
**Author:** [@DilhanideSri](https://forum.mothur.org/u/DilhanideSri)\ **Replies:** 2\ **Last updated:** [December 5, 2016, 8:47pm UTC](https://forum.mothur.org/t/nmds-biplot-to-show-both-samples-and-species-using-r/3053 "2016-12-05T20:47:41Z")
Dear Pat, I have successfully plotted NMDS to show sample sites using following functions. nmds\<-read.table(file=“stool.final.an.thetayc.0.03.lt.nmds.axes”, header=T) plot(nmds$axis1, nmds$axis2) Then I changed the c… --- ## [Installation](https://forum.mothur.org/t/installation/3013)
**Author:** [@sje062](https://forum.mothur.org/u/sje062)\ **Replies:** 0\ **Last updated:** [October 7, 2016, 7:31pm UTC](https://forum.mothur.org/t/installation/3013 "2016-10-07T19:31:45Z")
Anyone that may help with installation of Tax4Fun? R return me the message ‘qiimer’ missing, with the package from http://tax4fun.gobics.de/ Sigmund --- ## [Using MED (minimum entropy decomposition)](https://forum.mothur.org/t/using-med-minimum-entropy-decomposition/3011)
**Author:** [@kristinvh](https://forum.mothur.org/u/kristinvh)\ **Replies:** 0\ **Last updated:** [October 7, 2016, 9:49am UTC](https://forum.mothur.org/t/using-med-minimum-entropy-decomposition/3011 "2016-10-07T09:49:54Z")
Hi I am using 16s data generated from the Miseq illumina SOP and I would like to try MED (http://merenlab.org/2014/11/04/med/#the-manuscript) on the quality filtered-sequences (not the unique sequences). Which of the fi… --- ## [How to use mothur modules in python scripts](https://forum.mothur.org/t/how-to-use-mothur-modules-in-python-scripts/1386)
**Author:** [@bberger](https://forum.mothur.org/u/bberger)\ **Replies:** 7\ **Last updated:** [October 4, 2016, 3:04pm UTC](https://forum.mothur.org/t/how-to-use-mothur-modules-in-python-scripts/1386 "2016-10-04T15:04:45Z")
I would like to integrate mothur modules in my python scripts. How can I do this? How should I call mothur modules (e.g. sffinfo) in python? Thanks a lot for your help. --- ## [rarePlot in R ??](https://forum.mothur.org/t/rareplot-in-r/2986)
**Author:** [@nicolasc](https://forum.mothur.org/u/nicolasc)\ **Replies:** 1\ **Last updated:** [September 16, 2016, 2:46pm UTC](https://forum.mothur.org/t/rareplot-in-r/2986 "2016-09-16T14:46:09Z")
Hi everyone, I m trying to use some files created in mothur (outfile from the command rarefaction.single) in R. I found the package mothuR but this is not possible to install it on recent R version. Then I just unzip t… --- ## [.biom table for PICRUSt in Galaxy returning errors](https://forum.mothur.org/t/biom-table-for-picrust-in-galaxy-returning-errors/2970)
**Author:** [@met615](https://forum.mothur.org/u/met615)\ **Replies:** 1\ **Last updated:** [August 31, 2016, 1:51pm UTC](https://forum.mothur.org/t/biom-table-for-picrust-in-galaxy-returning-errors/2970 "2016-08-31T13:51:18Z")
Hi all, I’m not sure this is the best place to ask this, but I figured it was worth a shot. I generated a .biom table using the .cons.taxonomy I generated in mothur. I used the GreenGenes version specified by Galaxy (… --- ## [make biom.file to use this for core.diversity in QIIME](https://forum.mothur.org/t/make-biom-file-to-use-this-for-core-diversity-in-qiime/2968)
**Author:** [@kristinvh](https://forum.mothur.org/u/kristinvh)\ **Replies:** 1\ **Last updated:** [August 30, 2016, 12:17pm UTC](https://forum.mothur.org/t/make-biom-file-to-use-this-for-core-diversity-in-qiime/2968 "2016-08-30T12:17:08Z")
Hi I have used mothur (miseq sop) for illumina paired-end reads and want to make a biom.file and use this in QIIME. I used the following commands in mothur to create the biom.file: make.biom(shared=stability.file.trim… --- ## [importing dist matrix into R](https://forum.mothur.org/t/importing-dist-matrix-into-r/1266)
**Author:** [@Kendra](https://forum.mothur.org/u/Kendra)\ **Replies:** 7\ **Last updated:** [August 3, 2016, 2:42pm UTC](https://forum.mothur.org/t/importing-dist-matrix-into-r/1266 "2016-08-03T14:42:50Z")
I’m hoping some R wizard can help me. I’ve constructed distance matrices in mother (yeah for repeated subsampling capability) and now need to use them in R for further analyses. I can get the lower triangle data in but n… --- ## [Make.biom reulting an error](https://forum.mothur.org/t/make-biom-reulting-an-error/2939)
**Author:** [@Dilhanide](https://forum.mothur.org/u/Dilhanide)\ **Replies:** 1\ **Last updated:** [August 2, 2016, 5:12pm UTC](https://forum.mothur.org/t/make-biom-reulting-an-error/2939 "2016-08-02T17:12:41Z")
Dear mothur team, I have difficulties of running make.biom command in mothur since it results error message saying memory issue in the server, though the server had enough RAM for this (64Gb RAM). The command I used fo… --- ## [merge files from outside of mothur](https://forum.mothur.org/t/merge-files-from-outside-of-mothur/2906)
**Author:** [@Dilhanide](https://forum.mothur.org/u/Dilhanide)\ **Replies:** 1\ **Last updated:** [July 4, 2016, 4:37pm UTC](https://forum.mothur.org/t/merge-files-from-outside-of-mothur/2906 "2016-07-04T16:37:31Z")
Dear Pat, I got DNA sequences from Illumina Miseq V3-V4 region-paired reads (now I know sequencing that region was a disaster) and the reverse reads had poor quality and using mothur I went up to cluster.split and then… --- ## [Mothur and Picrust convert Silva analysis to GreenGenes biom](https://forum.mothur.org/t/mothur-and-picrust-convert-silva-analysis-to-greengenes-biom/2012)
**Author:** [@dsobral](https://forum.mothur.org/u/dsobral)\ **Replies:** 7\ **Last updated:** [May 25, 2016, 9:05pm UTC](https://forum.mothur.org/t/mothur-and-picrust-convert-silva-analysis-to-greengenes-biom/2012 "2016-05-25T21:05:58Z")
Hello, I’m trying to use results from Mothur into Picrust. I run my sample roughly as defined in the MiSeq SOP: http://www.mothur.org/wiki/MiSeq\_SOP I use the Silva database as in the SOP and go all the way until the… --- ## [Generalized UniFrac CRAN Package](https://forum.mothur.org/t/generalized-unifrac-cran-package/2839)
**Author:** [@ggs422](https://forum.mothur.org/u/ggs422)\ **Replies:** 1\ **Last updated:** [May 12, 2016, 8:10pm UTC](https://forum.mothur.org/t/generalized-unifrac-cran-package/2839 "2016-05-12T20:10:56Z")
Background I would like to calculate generalized UniFrac distances (1) for a microbial community produced from the MiSeq SOP (2). All of the authors’ example code works (3), but I do not know how to load a tree from Mot… --- ## [mothur and real-time PCR](https://forum.mothur.org/t/mothur-and-real-time-pcr/2338)
**Author:** [@sapou](https://forum.mothur.org/u/sapou)\ **Replies:** 2\ **Last updated:** [May 3, 2016, 6:35am UTC](https://forum.mothur.org/t/mothur-and-real-time-pcr/2338 "2016-05-03T06:35:09Z")
I have been looking into the gut bacterial communities of ants and using 454 or Miseq 16S I get pretty good insights however I dont get any information about the actual bacterial levels as during the library prep everyth… --- ## [Using Mothur in an IPython Notebook](https://forum.mothur.org/t/using-mothur-in-an-ipython-notebook/2824)
**Author:** [@botanick](https://forum.mothur.org/u/botanick)\ **Replies:** 5\ **Last updated:** [April 29, 2016, 2:39pm UTC](https://forum.mothur.org/t/using-mothur-in-an-ipython-notebook/2824 "2016-04-29T14:39:09Z")
Hi Forum, I’m new here, so I hope that this the right place to put this. I am also new to Mother, but I have been using IPython for a while now. I saw this tweet the tweet: https://twitter.com/patschloss/status/454224… --- ## [convert tax.summary file into krona](https://forum.mothur.org/t/convert-tax-summary-file-into-krona/2797)
**Author:** [@ch3coch3](https://forum.mothur.org/u/ch3coch3)\ **Replies:** 2\ **Last updated:** [April 28, 2016, 7:24pm UTC](https://forum.mothur.org/t/convert-tax-summary-file-into-krona/2797 "2016-04-28T19:24:46Z")
Hi all, I tried to play with krona and it’s my understanding that we can use the xxx\_list.0.03.cons.tax.summary file from mothur and krona excel template to make krona .html file for visualization. I even found a py scr… --- ## [SILVAngs and mothur](https://forum.mothur.org/t/silvangs-and-mothur/2815)
**Author:** [@apgajigan](https://forum.mothur.org/u/apgajigan)\ **Replies:** 0\ **Last updated:** [April 19, 2016, 6:22am UTC](https://forum.mothur.org/t/silvangs-and-mothur/2815 "2016-04-19T06:22:21Z")
Hi all, I would like ask if someone have tried using mothur to calculate diversity indices using SILVAngs output? If yes, posting the brief methodology will be very helpful. Thank for your time, Andrian --- ## [R vegan NMDS vs mothur NMDS](https://forum.mothur.org/t/r-vegan-nmds-vs-mothur-nmds/2795)
**Author:** [@Geroca](https://forum.mothur.org/u/Geroca)\ **Replies:** 4\ **Last updated:** [April 18, 2016, 2:26pm UTC](https://forum.mothur.org/t/r-vegan-nmds-vs-mothur-nmds/2795 "2016-04-18T14:26:13Z")
Hi all, I’m still not too experienced with mothur but thanks to my co-worker instructions, 454 SOP and this forum threads (which I’ve found really helpful), I’ve been able to process my 16S rRNA sequences, obtained by … --- ## [R script for 3d PCOA plotting?](https://forum.mothur.org/t/r-script-for-3d-pcoa-plotting/2791)
**Author:** [@ch3coch3](https://forum.mothur.org/u/ch3coch3)\ **Replies:** 1\ **Last updated:** [April 3, 2016, 8:47pm UTC](https://forum.mothur.org/t/r-script-for-3d-pcoa-plotting/2791 "2016-04-03T20:47:42Z")
Hi all, I got the pcoa results from mothur, named “xx.pcoa.axes”. I would like to plot the results as the 3d pcoa plot. Thanks to the script provided by dwaite, I was able to plot 2d pcoa. The code as below, in case it … --- ## [importing itag sequences into mothur from JGI](https://forum.mothur.org/t/importing-itag-sequences-into-mothur-from-jgi/2680)
**Author:** [@spaver](https://forum.mothur.org/u/spaver)\ **Replies:** 3\ **Last updated:** [February 16, 2016, 11:31am UTC](https://forum.mothur.org/t/importing-itag-sequences-into-mothur-from-jgi/2680 "2016-02-16T11:31:43Z")
I have illumina sequences from JGI that have been run through the iTagger pipeline that I would like to run through mothur and am searching for the most logical entry point into mothur. For raw data, I have one interlea… [Previous page](https://forum.mothur.org/c/integrating-mothur-with-other-programs/12.md) [Next page](https://forum.mothur.org/c/integrating-mothur-with-other-programs/12.md?page=2)