# Integrating mothur with other programs **URL:** https://forum.mothur.org/c/integrating-mothur-with-other-programs/12.md?page=2 [Latest](https://forum.mothur.org/latest.md) · [Categories](https://forum.mothur.org/categories.md) **Page:** 3 --- ## [STAMP](https://forum.mothur.org/t/stamp/2607)
**Author:** [@julcham1](https://forum.mothur.org/u/julcham1)\ **Replies:** 1\ **Last updated:** [January 13, 2016, 9:35am UTC](https://forum.mothur.org/t/stamp/2607 "2016-01-13T09:35:08Z")
Hi, Does anyone tried STAMP with mothur ? I have problem to run it… how did you make your group file ? Thanks, Julien --- ## [Script to convert taxonomy summaries to Krona-compatible XML](https://forum.mothur.org/t/script-to-convert-taxonomy-summaries-to-krona-compatible-xml/1591)
**Author:** [@adamc83](https://forum.mothur.org/u/adamc83)\ **Replies:** 3\ **Last updated:** [November 11, 2015, 9:47pm UTC](https://forum.mothur.org/t/script-to-convert-taxonomy-summaries-to-krona-compatible-xml/1591 "2015-11-11T21:47:01Z")
I wrote a script to convert mothur’s taxonomy summaries into a format compatible with Krona’s XML importer. Check it out: https://github.com/accaldwell/mothur\_krona Feel free to send me any bugs, fixes, or suggestions. … --- ## [calculating unifrac distance between subsets of communities](https://forum.mothur.org/t/calculating-unifrac-distance-between-subsets-of-communities/2573)
**Author:** [@ling](https://forum.mothur.org/u/ling)\ **Replies:** 2\ **Last updated:** [October 20, 2015, 3:46pm UTC](https://forum.mothur.org/t/calculating-unifrac-distance-between-subsets-of-communities/2573 "2015-10-20T15:46:36Z")
Hello, I’m trying to calculate the unifrac distance between OTUs categorized to different subsets within the same community. For example, I have communities A, B, and C made of OTUs 1, 2, 3, 4, 5,6,7,8,9,10. Now I need … --- ## [Merging mothur biom and QIIME biom](https://forum.mothur.org/t/merging-mothur-biom-and-qiime-biom/2484)
**Author:** [@arghya1611](https://forum.mothur.org/u/arghya1611)\ **Replies:** 1\ **Last updated:** [August 11, 2015, 4:46pm UTC](https://forum.mothur.org/t/merging-mothur-biom-and-qiime-biom/2484 "2015-08-11T16:46:07Z")
Hi Can anyone advise me if the biom file generated in mothur from .shared (having used the greengenes 13\_8\_99 database for classify.seqs) b merged wiht biom files generated in OTU picking scripts in QIIME (as open\_refer… --- ## [Problem Qiime/mothur different results](https://forum.mothur.org/t/problem-qiime-mothur-different-results/2472)
**Author:** [@PapaSmurf](https://forum.mothur.org/u/PapaSmurf)\ **Replies:** 5\ **Last updated:** [August 4, 2015, 7:48am UTC](https://forum.mothur.org/t/problem-qiime-mothur-different-results/2472 "2015-08-04T07:48:29Z")
Hi everybody, I am facing an issue with my dataset. I used 454 to sequence g23 viral protein from sea water samples. g23 analysis on new sequencing (ok, not that new anymore) technologies is still not really developed,… --- ## [explicit log for picrust otu conversion](https://forum.mothur.org/t/explicit-log-for-picrust-otu-conversion/2372)
**Author:** [@willnotburn](https://forum.mothur.org/u/willnotburn)\ **Replies:** 0\ **Last updated:** [May 29, 2015, 3:07pm UTC](https://forum.mothur.org/t/explicit-log-for-picrust-otu-conversion/2372 "2015-05-29T15:07:20Z")
Hi All, I’m using the picrust option in make.biom with great pleasure and no problems. However, I’d like to track which of the original 97% clustered OTUs were converted to picrust-compatible Greengenes phylotypes. The… --- ## [Using biom from QIIME to make venn diagram](https://forum.mothur.org/t/using-biom-from-qiime-to-make-venn-diagram/2341)
**Author:** [@pencey](https://forum.mothur.org/u/pencey)\ **Replies:** 0\ **Last updated:** [April 2, 2015, 6:26pm UTC](https://forum.mothur.org/t/using-biom-from-qiime-to-make-venn-diagram/2341 "2015-04-02T18:26:37Z")
I have a biom file with individual samples from QIIME. a mapping file with a column containing groups based on which I want to collapse samples I want to convert the biom file into .shared file group samples in the … --- ## [unclassified](https://forum.mothur.org/t/unclassified/2314)
**Author:** [@sje062](https://forum.mothur.org/u/sje062)\ **Replies:** 1\ **Last updated:** [March 24, 2015, 12:42pm UTC](https://forum.mothur.org/t/unclassified/2314 "2015-03-24T12:42:27Z")
Hi mothur forum, may I have a reply on how to improve on unclassified in the taxonomy file, if possible? For example, can output from megablast become a taxonomy file? Sigmund --- ## [make.shared(biom=otu\_table.biom)](https://forum.mothur.org/t/make-shared-biom-otu-table-biom/1305)
**Author:** [@marcosjaune](https://forum.mothur.org/u/marcosjaune)\ **Replies:** 11\ **Last updated:** [February 17, 2015, 9:36am UTC](https://forum.mothur.org/t/make-shared-biom-otu-table-biom/1305 "2015-02-17T09:36:27Z")
Hi mothur users, I have a problem and i hope somebody can help me. I have an otu\_table.biom file obtained with qiime and i want to use it in mothur to make an alpha-diversity analysis. So, i am trying with make.shared(b… --- ## [LoTuS integration and use](https://forum.mothur.org/t/lotus-integration-and-use/2061)
**Author:** [@Somebodyatthedoor](https://forum.mothur.org/u/Somebodyatthedoor)\ **Replies:** 1\ **Last updated:** [October 8, 2014, 2:57pm UTC](https://forum.mothur.org/t/lotus-integration-and-use/2061 "2014-10-08T14:57:19Z")
Hi, Just wondering what the general opinion on LoTuS (Hildebrand et al. 2014, Microbiome) was and how easily it could be used with MOTHUR? It relies on UPARSE which I know isn’t that popular with a lot of people round … --- ## [Mothur and QIIME (trimming)](https://forum.mothur.org/t/mothur-and-qiime-trimming/2037)
**Author:** [@jini49](https://forum.mothur.org/u/jini49)\ **Replies:** 1\ **Last updated:** [September 22, 2014, 12:27pm UTC](https://forum.mothur.org/t/mothur-and-qiime-trimming/2037 "2014-09-22T12:27:53Z")
Hi All, I used Mothur to trim a set of 454 sequences (used min and max length, qaverage=25, maxambig=0). I also used the Chimera Slayer and filter.seqs (on Mothur). I then imported a subset of these sequences into QII… --- ## [opening shared.file in excel - does not fully upload](https://forum.mothur.org/t/opening-shared-file-in-excel-does-not-fully-upload/1955)
**Author:** [@azel](https://forum.mothur.org/u/azel)\ **Replies:** 5\ **Last updated:** [August 9, 2014, 3:54pm UTC](https://forum.mothur.org/t/opening-shared-file-in-excel-does-not-fully-upload/1955 "2014-08-09T15:54:43Z")
Hello all, I currently have an OTU table that was generated with the make.shared command, and it contains over 50,000 OTU’s. I would like to view this table in excel, however there are too many columns and as a result, … --- ## [Mothur and RDP](https://forum.mothur.org/t/mothur-and-rdp/1831)
**Author:** [@jini49](https://forum.mothur.org/u/jini49)\ **Replies:** 1\ **Last updated:** [May 9, 2014, 12:29pm UTC](https://forum.mothur.org/t/mothur-and-rdp/1831 "2014-05-09T12:29:36Z")
Hi everyone, I’m very very new to analyzing pyrosequencing results. I’m starting to understand how trimming etc. works. A colleague suggested comparing my mothur results to the RDP pyrosequencing pipeline results and … --- ## [The EMP, QIIME and Mothur](https://forum.mothur.org/t/the-emp-qiime-and-mothur/1425)
**Author:** [@Shaunson26](https://forum.mothur.org/u/Shaunson26)\ **Replies:** 9\ **Last updated:** [May 2, 2014, 12:02am UTC](https://forum.mothur.org/t/the-emp-qiime-and-mothur/1425 "2014-05-02T00:02:53Z")
So, I’m dealing with data from “The Earth Microbiome Project”… Illumina HiSeq @ 100bp… I decided to run the data through Mothur rather than used the QIIME analysed data they provide. They say; \_97% OTUs are picked in th… --- ## [taxonomy outline](https://forum.mothur.org/t/taxonomy-outline/1811)
**Author:** [@sje062](https://forum.mothur.org/u/sje062)\ **Replies:** 0\ **Last updated:** [April 23, 2014, 7:33pm UTC](https://forum.mothur.org/t/taxonomy-outline/1811 "2014-04-23T19:33:07Z")
It would be helpful with a tip on where to find an updated file to use as template in classification (e.g., silva.bacteria.fasta). Exporting from ARB I have not found the option that makes a fasta file I can use direc… --- ## [Using cutadapt for primers](https://forum.mothur.org/t/using-cutadapt-for-primers/1737)
**Author:** [@Somebodyatthedoor](https://forum.mothur.org/u/Somebodyatthedoor)\ **Replies:** 1\ **Last updated:** [March 11, 2014, 12:05pm UTC](https://forum.mothur.org/t/using-cutadapt-for-primers/1737 "2014-03-11T12:05:15Z")
Hi, I’ve been using cutadapt to remove primers before running make.contigs on my Miseq data due to some problems using the inbuilt commands in mothur. Cutadapt removes sequences which do not contain the primer (with an … --- ## [Mothur Linux latest version](https://forum.mothur.org/t/mothur-linux-latest-version/1660)
**Author:** [@nabss](https://forum.mothur.org/u/nabss)\ **Replies:** 2\ **Last updated:** [January 28, 2014, 3:19pm UTC](https://forum.mothur.org/t/mothur-linux-latest-version/1660 "2014-01-28T15:19:51Z")
I am new in the forum, sorry if this is not the better place for the question… I had just downloaded the latest version for linux\_64bit (without readline), however when I run it in the console it says that it is v.1.22.2… --- ## [Combine mothur and picrust](https://forum.mothur.org/t/combine-mothur-and-picrust/1632)
**Author:** [@doodlehzq123](https://forum.mothur.org/u/doodlehzq123)\ **Replies:** 1\ **Last updated:** [January 7, 2014, 2:16pm UTC](https://forum.mothur.org/t/combine-mothur-and-picrust/1632 "2014-01-07T14:16:30Z")
Picrust is a recent published tool that can infer biological pathways from 16S RNA. In spite that WGS seems better for this purpose, it still shows additional information. (Picrust:Predictive functional profiling of micr… --- ## [Java-IO-Question](https://forum.mothur.org/t/java-io-question/1599)
**Author:** [@Hiwi](https://forum.mothur.org/u/Hiwi)\ **Replies:** 4\ **Last updated:** [December 5, 2013, 2:15pm UTC](https://forum.mothur.org/t/java-io-question/1599 "2013-12-05T14:15:33Z")
Hi, I am developing a tool simmilar to the mothurGUI-toolkit. My actual problem is, that I try to interact with mothur from the virtual machine via Input/Output-streams. I successful started mothur from java ( wihtout… --- ## [Default Exit value and command line options](https://forum.mothur.org/t/default-exit-value-and-command-line-options/1600)
**Author:** [@Hiwi](https://forum.mothur.org/u/Hiwi)\ **Replies:** 3\ **Last updated:** [December 5, 2013, 2:03pm UTC](https://forum.mothur.org/t/default-exit-value-and-command-line-options/1600 "2013-12-05T14:03:11Z")
Hi, What is the default exit value of mothur if everything runs fine? Are there some command line arguments I can specify? Regards, TL --- ## [Keeping Illumina headers unchanged for non-Mothur use](https://forum.mothur.org/t/keeping-illumina-headers-unchanged-for-non-mothur-use/1348)
**Author:** [@dylansmith17](https://forum.mothur.org/u/dylansmith17)\ **Replies:** 5\ **Last updated:** [May 17, 2013, 5:10pm UTC](https://forum.mothur.org/t/keeping-illumina-headers-unchanged-for-non-mothur-use/1348 "2013-05-17T17:10:27Z")
After commands like trim.seqs, screen.seqs, make.contigs, etc., Mothur always tells you “I changed your : to - for ease in downstream analyses”. The only problem is that other programs, e.g. Pandaseq (for pairing R1 and… [Previous page](https://forum.mothur.org/c/integrating-mothur-with-other-programs/12.md?page=1)