# \#phylogeny **URL:** https://forum.qiime2.org/tag/phylogeny/57.md [Latest](https://forum.qiime2.org/latest.md) · [Categories](https://forum.qiime2.org/categories.md) · [Tags](https://forum.qiime2.org/tags.md) --- ## [Remove Unassigned ASV for Tree construction](https://forum.qiime2.org/t/remove-unassigned-asv-for-tree-construction/33866)
**Author:** [@Alessandro](https://forum.qiime2.org/u/Alessandro)\ **Replies:** 3\ **Last updated:** [December 16, 2025, 2:43pm UTC](https://forum.qiime2.org/t/remove-unassigned-asv-for-tree-construction/33866 "2025-12-16T14:43:33Z")
Hi everyone, I don’t have much experience with statistical and phylogenetic analyses, and I have only recently started using QIIME 2. By following the suggested tutorials, I reached the step of building a phylogenetic tr… --- ## [ITS phylogeny using iq-tree](https://forum.qiime2.org/t/its-phylogeny-using-iq-tree/33759)
**Author:** [@scilexenko](https://forum.qiime2.org/u/scilexenko)\ **Replies:** 4\ **Last updated:** [November 13, 2025, 2:26pm UTC](https://forum.qiime2.org/t/its-phylogeny-using-iq-tree/33759 "2025-11-13T14:26:33Z")
Hello QIIME 2 team and community, I’m working on fungal ITS data (from soil and tree microbiomes) and would like to include phylogenetic metrics such as WUniFrac in my diversity analyses (and not only; for example for t… --- ## [how to phylogenetically analyse 16S genes recovered from metagenome?](https://forum.qiime2.org/t/how-to-phylogenetically-analyse-16s-genes-recovered-from-metagenome/32643)
**Author:** [@peccat](https://forum.qiime2.org/u/peccat)\ **Replies:** 2\ **Last updated:** [March 3, 2025, 1:42pm UTC](https://forum.qiime2.org/t/how-to-phylogenetically-analyse-16s-genes-recovered-from-metagenome/32643 "2025-03-03T13:42:53Z")
Hi there, I recently reconstructed or identified some 16S genes using tools like MATAM or barrnap, respectively. I noticed the resulting fragments of 16S gene varied across samples or MAGs, generally with a divergent le… --- ## [Introducing Greengenes2 2022.10](https://forum.qiime2.org/t/introducing-greengenes2-2022-10/25291)
**Author:** [@wasade](https://forum.qiime2.org/u/wasade)\ **Replies:** 71\ **Last updated:** [October 11, 2024, 10:01pm UTC](https://forum.qiime2.org/t/introducing-greengenes2-2022-10/25291 "2024-10-11T22:01:51Z")
IMPORTANT: Greengenes2 2022.10 has been replaced with 2024.09. More information can be found here. The commands and examples noted within this tutorial remain relevant though. Introduction We are excited to announce a n… --- ## [Help with filtering phylogeny based on feature table: Not a single fragment of your table is part of your tree. The resulting table would be empty.](https://forum.qiime2.org/t/help-with-filtering-phylogeny-based-on-feature-table-not-a-single-fragment-of-your-table-is-part-of-your-tree-the-resulting-table-would-be-empty/30791)
**Author:** [@kristend](https://forum.qiime2.org/u/kristend)\ **Replies:** 2\ **Last updated:** [July 15, 2024, 4:23pm UTC](https://forum.qiime2.org/t/help-with-filtering-phylogeny-based-on-feature-table-not-a-single-fragment-of-your-table-is-part-of-your-tree-the-resulting-table-would-be-empty/30791 "2024-07-15T16:23:12Z")
Hi, I'm running QIIME2 v2024.5.1 on our university computer cluster. I've got a problem that I'm not sure you can solve, but I'm hoping someone can give me some tools to help diagnose where the issue is. I've gone throu… --- ## [Phylogeny error](https://forum.qiime2.org/t/phylogeny-error/30600)
**Author:** [@EugeniaSH](https://forum.qiime2.org/u/EugeniaSH)\ **Replies:** 4\ **Last updated:** [June 25, 2024, 2:31pm UTC](https://forum.qiime2.org/t/phylogeny-error/30600 "2024-06-25T14:31:34Z")
Hello, I am using Qiime2-2022.11 , after more than 24 hrs of running the phylogeny command : qiime phylogeny align-to-tree-mafft-fasttree --i-sequences rep-seqs\_juntas3.qza --o-alignment aligned-rep-seq\_juntas3f.qz… --- ## [Core-metrics (Plugin error from diversity)](https://forum.qiime2.org/t/core-metrics-plugin-error-from-diversity/29402)
**Author:** [@caca](https://forum.qiime2.org/u/caca)\ **Replies:** 8\ **Last updated:** [March 1, 2024, 5:33am UTC](https://forum.qiime2.org/t/core-metrics-plugin-error-from-diversity/29402 "2024-03-01T05:33:29Z")
hi everyone, Im trying to make alpha and beta diversity but when i run the following : qiime diversity core-metrics-phylogenetic --i-phylogeny Lombok\_v9\_18-rooted-tree.qza --i-table Lombok\_v9\_18\_table.qza --p-sampl… --- ## [Error occured while running for MAFFT in qiime2](https://forum.qiime2.org/t/error-occured-while-running-for-mafft-in-qiime2/29269)
**Author:** [@pulak](https://forum.qiime2.org/u/pulak)\ **Replies:** 7\ **Last updated:** [February 22, 2024, 4:35pm UTC](https://forum.qiime2.org/t/error-occured-while-running-for-mafft-in-qiime2/29269 "2024-02-22T16:35:31Z")
The following problem occured while running for MAFFT sequence alignment for rep-seqs.qza file in HPC. "Plugin error from phylogeny: Command '\['mafft', '--preservecase', '--inputorder', '--thread', '1', '/tmp/qiime2/pu… --- ## [ASVs of the same genus in different branches on the phylogenetic tree](https://forum.qiime2.org/t/asvs-of-the-same-genus-in-different-branches-on-the-phylogenetic-tree/29293)
**Author:** [@eraysahin](https://forum.qiime2.org/u/eraysahin)\ **Replies:** 2\ **Last updated:** [February 19, 2024, 5:54pm UTC](https://forum.qiime2.org/t/asvs-of-the-same-genus-in-different-branches-on-the-phylogenetic-tree/29293 "2024-02-19T17:54:24Z")
Hello, I constructed my phylogenetic tree using "qiime phylogeny align-to-tree-mafft-fasttree", and exported rooted tree. For taxonomic assignment of the ASVs, I produced weighted classifier of SILVA 138 SSURef NR99. Af… --- ## [qiime vsearch cluster-features-open-reference issue](https://forum.qiime2.org/t/qiime-vsearch-cluster-features-open-reference-issue/29131)
**Author:** [@devenderarora](https://forum.qiime2.org/u/devenderarora)\ **Replies:** 11\ **Last updated:** [February 15, 2024, 6:23pm UTC](https://forum.qiime2.org/t/qiime-vsearch-cluster-features-open-reference-issue/29131 "2024-02-15T18:23:19Z")
Hello Qiime members, I am trying to run "cluster-features-open-reference" for diversity analysis. We would like to run differential abundance analysis on OTU corresponding to denovo ref-sequence but there is no option t… --- ## [Generating phylogenic tree for diversity analyses](https://forum.qiime2.org/t/generating-phylogenic-tree-for-diversity-analyses/28319)
**Author:** [@TM3197](https://forum.qiime2.org/u/TM3197)\ **Replies:** 4\ **Last updated:** [November 20, 2023, 6:57am UTC](https://forum.qiime2.org/t/generating-phylogenic-tree-for-diversity-analyses/28319 "2023-11-20T06:57:53Z")
Hi, I am running the following script but getting an error. Do you have any suggestions to troubleshoot? Thank you. $ qiime phylogeny align-to-tree-mafft-fasttree \\ --i-sequences oral\_rep-seqs-DADA2.qza \\ --o-align… --- ## [Greengenes2 feature in table not found in tree during beta-rarefaction](https://forum.qiime2.org/t/greengenes2-feature-in-table-not-found-in-tree-during-beta-rarefaction/27361)
**Author:** [@MarlydEMejia](https://forum.qiime2.org/u/MarlydEMejia)\ **Replies:** 6\ **Last updated:** [September 5, 2023, 3:45pm UTC](https://forum.qiime2.org/t/greengenes2-feature-in-table-not-found-in-tree-during-beta-rarefaction/27361 "2023-09-05T15:45:59Z")
Good afternoon! I am using Qiime2 in a conda env and ran the beta-rarefaction plug-in: qiime diversity beta-rarefaction --i-table OTU\_filtdecontamfilt\_long\_baseline.qza --i-phylogeny 2022.10.phylogeny.asv.nwk.qza … --- ## [Visualizing phylogenetic trees](https://forum.qiime2.org/t/visualizing-phylogenetic-trees/26449)
**Author:** [@MaxEdge](https://forum.qiime2.org/u/MaxEdge)\ **Replies:** 2\ **Last updated:** [May 15, 2023, 7:19am UTC](https://forum.qiime2.org/t/visualizing-phylogenetic-trees/26449 "2023-05-15T07:19:59Z")
Hello forum. There is currently no visualizer for trees, but you can export the RootedPhylogeny as a .nwk that can be opened in other programs. The problem is the tree is annotated with the feature IDs, when ideally it … --- ## [plugin error from phylogeny - no such file or directory: mafft](https://forum.qiime2.org/t/plugin-error-from-phylogeny-no-such-file-or-directory-mafft/26349)
**Author:** [@fdebus](https://forum.qiime2.org/u/fdebus)\ **Replies:** 4\ **Last updated:** [May 10, 2023, 1:22pm UTC](https://forum.qiime2.org/t/plugin-error-from-phylogeny-no-such-file-or-directory-mafft/26349 "2023-05-10T13:22:11Z")
Hello! I'm new to the use of Qiime2 and am trying to get the hang of if by following the Moving Pictures Tutorial. This forum has been a great help, so I first wanted to thank all of you already! The problem I face is … --- ## [UniFrac and Phylogenetic Methods with Full-length 16S-ITS-23S Sequences](https://forum.qiime2.org/t/unifrac-and-phylogenetic-methods-with-full-length-16s-its-23s-sequences/25860)
**Author:** [@bosullivan](https://forum.qiime2.org/u/bosullivan)\ **Replies:** 3\ **Last updated:** [March 29, 2023, 10:43pm UTC](https://forum.qiime2.org/t/unifrac-and-phylogenetic-methods-with-full-length-16s-its-23s-sequences/25860 "2023-03-29T22:43:27Z")
Hi all, I have a question that I'm guessing most here haven't had to deal with. It concerns how to handle the analysis for sequencing data that contains the ITS sequence between the 16S and 23S rRNA genes (the full rRNA… --- ## [q2-phylogeny mafft job "killed"](https://forum.qiime2.org/t/q2-phylogeny-mafft-job-killed/25526)
**Author:** [@ysuzuki](https://forum.qiime2.org/u/ysuzuki)\ **Replies:** 10\ **Last updated:** [February 21, 2023, 2:35pm UTC](https://forum.qiime2.org/t/q2-phylogeny-mafft-job-killed/25526 "2023-02-21T14:35:39Z")
I would like to load rep-seqs.qza, which consists of 24 100k reads samples, for phylogeny analysis, but I get an error. I would appreciate if you could tell me how to deal with this problem. #input command qiime phylog… --- ## [Phylogenetic tree tools](https://forum.qiime2.org/t/phylogenetic-tree-tools/25244)
**Author:** [@Antani](https://forum.qiime2.org/u/Antani)\ **Replies:** 10\ **Last updated:** [February 10, 2023, 5:48pm UTC](https://forum.qiime2.org/t/phylogenetic-tree-tools/25244 "2023-02-10T17:48:04Z")
Hello everybody, I'm working on a metabarcoding dataset of ITS1. I just finished classifying my sequences and plotted how my community fared with taxa barplots. At this point I would also like to create a phylogenetic … --- ## [plugin error from phylogeny raxml (default): returned non-zero exit status 255](https://forum.qiime2.org/t/plugin-error-from-phylogeny-raxml-default-returned-non-zero-exit-status-255/24765)
**Author:** [@Shuqi](https://forum.qiime2.org/u/Shuqi)\ **Replies:** 6\ **Last updated:** [January 3, 2023, 8:28pm UTC](https://forum.qiime2.org/t/plugin-error-from-phylogeny-raxml-default-returned-non-zero-exit-status-255/24765 "2023-01-03T20:28:54Z")
Hello, I tried to construct phylogenetic tree using raxml and fasttree so I can make comparison between the two outputs. However, the plugin "phylogeny align-to-tree-mafft-raxml" returned non-zero exit status 255 while … --- ## [Make phylogenetic tree based on sequence](https://forum.qiime2.org/t/make-phylogenetic-tree-based-on-sequence/24914)
**Author:** [@Nelli](https://forum.qiime2.org/u/Nelli)\ **Replies:** 4\ **Last updated:** [December 5, 2022, 6:19am UTC](https://forum.qiime2.org/t/make-phylogenetic-tree-based-on-sequence/24914 "2022-12-05T06:19:26Z")
Hey there, I have used the dada2 algorithm for analyzing fastq files. Now I want to switch to qiime2 for downstream analysis. I have changed the ASV table into a feature table.qza format, and also I have metadata.tsv fi… --- ## [Qiime 2 version of Qiime1 "pick\_rep\_set.py" for picking representative OTU sequences](https://forum.qiime2.org/t/qiime-2-version-of-qiime1-pick-rep-set-py-for-picking-representative-otu-sequences/24813)
**Author:** [@Phoebe\_Cunningham](https://forum.qiime2.org/u/Phoebe_Cunningham)\ **Replies:** 3\ **Last updated:** [November 22, 2022, 1:27pm UTC](https://forum.qiime2.org/t/qiime-2-version-of-qiime1-pick-rep-set-py-for-picking-representative-otu-sequences/24813 "2022-11-22T13:27:29Z")
Hi there, I am trying to pick representative sequences from the OTU table I have created so that I have one representative sequence for each OTU cluster, so I have a smaller OTU table that can then be used to generate a… --- ## [Converting file from .tre to .nwk?](https://forum.qiime2.org/t/converting-file-from-tre-to-nwk/23954)
**Author:** [@agonzales](https://forum.qiime2.org/u/agonzales)\ **Replies:** 4\ **Last updated:** [August 28, 2022, 4:00pm UTC](https://forum.qiime2.org/t/converting-file-from-tre-to-nwk/23954 "2022-08-28T16:00:42Z")
Hi everyone, I have a phylogeny file as a: .tre, and need to convert it to a .nwk. Any ideas on how to do this? thanks --- ## [q2-phylogeny for vertebrates](https://forum.qiime2.org/t/q2-phylogeny-for-vertebrates/23955)
**Author:** [@DeannaB](https://forum.qiime2.org/u/DeannaB)\ **Replies:** 4\ **Last updated:** [August 25, 2022, 5:35pm UTC](https://forum.qiime2.org/t/q2-phylogeny-for-vertebrates/23955 "2022-08-25T17:35:18Z")
Hello, I'm working with Illumina short reads of fish environmental DNA (using 12S MiFish primers). I've successfully generated a de novo phylogenetic tree of OTU clusters using qiime phylogeny fasttree after generating a… --- ## [Phylogenetic analysis of Nanopore 16S reads. How many subsampled reads will do?](https://forum.qiime2.org/t/phylogenetic-analysis-of-nanopore-16s-reads-how-many-subsampled-reads-will-do/23265)
**Author:** [@hoohugokim](https://forum.qiime2.org/u/hoohugokim)\ **Replies:** 7\ **Last updated:** [July 30, 2022, 10:57pm UTC](https://forum.qiime2.org/t/phylogenetic-analysis-of-nanopore-16s-reads-how-many-subsampled-reads-will-do/23265 "2022-07-30T22:57:46Z")
Hello! :person\_raising\_hand: It is my first time posting in the QIIME2 forum, which means my experience with QIIME2 has been only great so far without much ado. Recently I'm processing some Nanopore 16S V1–V9 reads and a… --- ## [Plugin error from phylogeny qiime2-2022.2](https://forum.qiime2.org/t/plugin-error-from-phylogeny-qiime2-2022-2/23728)
**Author:** [@Shaminur](https://forum.qiime2.org/u/Shaminur)\ **Replies:** 1\ **Last updated:** [July 28, 2022, 7:45pm UTC](https://forum.qiime2.org/t/plugin-error-from-phylogeny-qiime2-2022-2/23728 "2022-07-28T19:45:06Z")
I am using qiime2-2022.2 While running the phylogeny, qiime phylogeny align-to-tree-mafft-fasttree --i-sequences 1\_7b\_rep-seqs-dn-99.qza --output-dir mafft-fasttree-output We got the error: Plugin error from ph… --- ## [Plugin error from diversity to get alpha and beta diversity](https://forum.qiime2.org/t/plugin-error-from-diversity-to-get-alpha-and-beta-diversity/23642)
**Author:** [@kevin\_SalOrt](https://forum.qiime2.org/u/kevin_SalOrt)\ **Replies:** 2\ **Last updated:** [July 21, 2022, 6:17pm UTC](https://forum.qiime2.org/t/plugin-error-from-diversity-to-get-alpha-and-beta-diversity/23642 "2022-07-21T18:17:51Z")
hi everyone! Im trying to make alpha and beta diversity but when i run the following: qiime diversity core-metrics-phylogenetic --i-phylogeny diversity/rooted\_tree.qza --i-table ft\_norm.qza --m-metadata-file manifest.t… --- ## [Bulding a phylogeny using taxonomy](https://forum.qiime2.org/t/bulding-a-phylogeny-using-taxonomy/22600)
**Author:** [@Omer](https://forum.qiime2.org/u/Omer)\ **Replies:** 5\ **Last updated:** [March 29, 2022, 3:49pm UTC](https://forum.qiime2.org/t/bulding-a-phylogeny-using-taxonomy/22600 "2022-03-29T15:49:40Z")
Hi, a question as a pretty new user of QIIME2 (and a researcher in the microbiome world). I'm working with a collabrator, and recived from him, after he DADA2 processed it, table containing the observed ASV's per sample… --- ## [qiime phylogeny](https://forum.qiime2.org/t/qiime-phylogeny/22597)
**Author:** [@No.77](https://forum.qiime2.org/u/No.77)\ **Replies:** 1\ **Last updated:** [March 28, 2022, 2:30pm UTC](https://forum.qiime2.org/t/qiime-phylogeny/22597 "2022-03-28T14:30:55Z")
Excuse me, I would like to ask what is the difference between the iqtree,fatstree and ramxl when using "phylogeny" to build a phylogenetic tree? --- ## [Changing tip labels on rooted-tree.qza from sequence identifiers to SILVA taxa annotations using R](https://forum.qiime2.org/t/changing-tip-labels-on-rooted-tree-qza-from-sequence-identifiers-to-silva-taxa-annotations-using-r/13977)
**Author:** [@buserj](https://forum.qiime2.org/u/buserj)\ **Replies:** 10\ **Last updated:** [March 23, 2022, 12:28am UTC](https://forum.qiime2.org/t/changing-tip-labels-on-rooted-tree-qza-from-sequence-identifiers-to-silva-taxa-annotations-using-r/13977 "2022-03-23T00:28:44Z")
Hello all, and thank you in advance for your time. My question relates to the rooted-tree.qza created in QIIME 2 2019.4, and how to change the tip labels from sequence IDs from DADA2 to taxa annotations, using R. I hav… --- ## [PD Mouse tutorial error in generating phylogenetic tree](https://forum.qiime2.org/t/pd-mouse-tutorial-error-in-generating-phylogenetic-tree/21561)
**Author:** [@EugeniaSH](https://forum.qiime2.org/u/EugeniaSH)\ **Replies:** 5\ **Last updated:** [December 21, 2021, 8:09pm UTC](https://forum.qiime2.org/t/pd-mouse-tutorial-error-in-generating-phylogenetic-tree/21561 "2021-12-21T20:09:41Z")
I am doing the Parkinson mouse tutorial , following the workshop in youtube I am on the Generating a phylogenetic tree part I copied the command from the tutorial page qiime fragment-insertion sepp --i-representativ… --- ## [Plugin error from diversity-lib: The table does not appear to be completely represented by the phylogeny](https://forum.qiime2.org/t/plugin-error-from-diversity-lib-the-table-does-not-appear-to-be-completely-represented-by-the-phylogeny/20220)
**Author:** [@guyshur](https://forum.qiime2.org/u/guyshur)\ **Replies:** 1\ **Last updated:** [July 22, 2021, 6:30pm UTC](https://forum.qiime2.org/t/plugin-error-from-diversity-lib-the-table-does-not-appear-to-be-completely-represented-by-the-phylogeny/20220 "2021-07-22T18:30:11Z")
Hello Q2 team, I am working with public OTU tables, and am trying to run some analyses. I collapsed a subset of Human Microbiome Project samples with Greengenes feature IDs with taxa collapse, and as a result I now have… [Next page](https://forum.qiime2.org/tag/phylogeny/57.md?match_all_tags=true&page=1&tags%5B%5D=phylogeny)