# \#beta **URL:** https://forum.qiime2.org/tag/beta/87.md [Latest](https://forum.qiime2.org/latest.md) · [Categories](https://forum.qiime2.org/categories.md) · [Tags](https://forum.qiime2.org/tags.md) --- ## [Shall I need to remove ASV with prevelance in one sample?](https://forum.qiime2.org/t/shall-i-need-to-remove-asv-with-prevelance-in-one-sample/33549)
**Author:** [@Brandon](https://forum.qiime2.org/u/Brandon)\ **Replies:** 4\ **Last updated:** [August 8, 2025, 6:55am UTC](https://forum.qiime2.org/t/shall-i-need-to-remove-asv-with-prevelance-in-one-sample/33549 "2025-08-08T06:55:40Z")
Hi Friends, I know that differential testing typically requires removing low-prevalence taxa. Do I also need to remove ASVs (inferred by DADA2) that are detected in only a single sample before performing alpha and beta… --- ## [Calculating dispersion using q2-convexhull](https://forum.qiime2.org/t/calculating-dispersion-using-q2-convexhull/32535)
**Author:** [@Daniela\_Perry1](https://forum.qiime2.org/u/Daniela_Perry1)\ **Replies:** 0\ **Last updated:** [February 15, 2025, 1:06am UTC](https://forum.qiime2.org/t/calculating-dispersion-using-q2-convexhull/32535 "2025-02-15T01:06:09Z")
q2-convexhull (github) Hi all, I'd like to share a plugin I've developed for calculating and visualizing dispersion in a dataset as done in Song et. al. 2021. q2-convexhull also provides standalone functionality in pytho… --- ## [How can I found the formula and source of the Canberra-Adkins distance measurement in “qiime diversity beta”?](https://forum.qiime2.org/t/how-can-i-found-the-formula-and-source-of-the-canberra-adkins-distance-measurement-in-qiime-diversity-beta/31869)
**Author:** [@yangyue](https://forum.qiime2.org/u/yangyue)\ **Replies:** 1\ **Last updated:** [November 13, 2024, 7:25am UTC](https://forum.qiime2.org/t/how-can-i-found-the-formula-and-source-of-the-canberra-adkins-distance-measurement-in-qiime-diversity-beta/31869 "2024-11-13T07:25:58Z")
Hello everyone, I am using the qiime2 command "qiime diversity beta" recently, but I cannot find the formula of the Canberra-Adkins distance measurement, who can help me to find its original paper or the source which ca… --- ## [scikit-bio.org has moved and links are broken](https://forum.qiime2.org/t/scikit-bio-org-has-moved-and-links-are-broken/31724)
**Author:** [@yangyue](https://forum.qiime2.org/u/yangyue)\ **Replies:** 2\ **Last updated:** [October 28, 2024, 1:15am UTC](https://forum.qiime2.org/t/scikit-bio-org-has-moved-and-links-are-broken/31724 "2024-10-28T01:15:06Z")
I wonder to know the formulas of qiime2 inherent alpha- and beta- diversity parameters, why the website https://data.qiime2.org/a\_diversity\_metrics can not entry at any time, and it shows http://scikit-bio.org is not saf… --- ## [Error beta rarefaction plugin](https://forum.qiime2.org/t/error-beta-rarefaction-plugin/30309)
**Author:** [@George\_kitundu](https://forum.qiime2.org/u/George_kitundu)\ **Replies:** 6\ **Last updated:** [May 28, 2024, 12:30pm UTC](https://forum.qiime2.org/t/error-beta-rarefaction-plugin/30309 "2024-05-28T12:30:50Z")
Hi everyone! I have been trying to perform beta-rarefaction analyses without success. My efforts to try to debug the error have yielded little success so far. I am using qiime2-amplicon-2024.2 conda version. Please advic… --- ## [Unweighted Unifrac looks weird](https://forum.qiime2.org/t/unweighted-unifrac-looks-weird/30280)
**Author:** [@MARTIN\_MIHULA](https://forum.qiime2.org/u/MARTIN_MIHULA)\ **Replies:** 1\ **Last updated:** [May 21, 2024, 1:44pm UTC](https://forum.qiime2.org/t/unweighted-unifrac-looks-weird/30280 "2024-05-21T13:44:55Z")
Dear all, I have a question for you. I generated a beta diversity emperor in two different environments: in QIIME2 (2024.2) and in R. Despite for Bray-Curtis, Jaccard and Weighted Unifrac the plot is basically the same,… --- ## [significant Permanova but non significant Permdisp](https://forum.qiime2.org/t/significant-permanova-but-non-significant-permdisp/29197)
**Author:** [@kevin\_SalOrt](https://forum.qiime2.org/u/kevin_SalOrt)\ **Replies:** 2\ **Last updated:** [February 9, 2024, 11:26pm UTC](https://forum.qiime2.org/t/significant-permanova-but-non-significant-permdisp/29197 "2024-02-09T23:26:32Z")
Hi friends! I have a doubt in statistical analysis, what does mean if i did a Permanova test and i got a pvalue of 0.01253 but, i ran a Permdisp test and i got a pvalue of 0.07? That could suggest a significant variatio… --- ## [weighted UniFrac result in different plot](https://forum.qiime2.org/t/weighted-unifrac-result-in-different-plot/28727)
**Author:** [@kubra](https://forum.qiime2.org/u/kubra)\ **Replies:** 1\ **Last updated:** [December 27, 2023, 1:17pm UTC](https://forum.qiime2.org/t/weighted-unifrac-result-in-different-plot/28727 "2023-12-27T13:17:08Z")
Hi, I run the code below: qiime diversity core-metrics-phylogenetic --i-phylogeny rooted-tree.qza --i-table table.qza --p-sampling-depth X --m-metadata-file sample-metadata.tsv --output-dir core-metrics-result… --- ## [Beta diversity graphs](https://forum.qiime2.org/t/beta-diversity-graphs/28577)
**Author:** [@TM3197](https://forum.qiime2.org/u/TM3197)\ **Replies:** 24\ **Last updated:** [December 18, 2023, 4:30am UTC](https://forum.qiime2.org/t/beta-diversity-graphs/28577 "2023-12-18T04:30:42Z")
Hi, bray\_curtis\_emperor.qzv (862.6 KB) jaccard\_emperor.qzv (862.5 KB) unweighted\_unifrac\_emperor.qzv (865.1 KB) weighted\_unifrac\_emperor.qzv (865.2 KB) Has anyone been able to determine why the data is clustered int… --- ## [microbiota analysis of insect species](https://forum.qiime2.org/t/microbiota-analysis-of-insect-species/28253)
**Author:** [@Linda\_Abenaim](https://forum.qiime2.org/u/Linda_Abenaim)\ **Replies:** 18\ **Last updated:** [November 28, 2023, 9:11am UTC](https://forum.qiime2.org/t/microbiota-analysis-of-insect-species/28253 "2023-11-28T09:11:56Z")
Hello everyone, I'm new to the world of Qiime2 and bioinformatics and I often encounter difficulties in processing my data. I'll explain exactly what I'm working on: I extracted gut microbial DNA from three different in… --- ## [significative adonis test, but no significance in paired adonis test?](https://forum.qiime2.org/t/significative-adonis-test-but-no-significance-in-paired-adonis-test/27807)
**Author:** [@kevin\_SalOrt](https://forum.qiime2.org/u/kevin_SalOrt)\ **Replies:** 3\ **Last updated:** [October 2, 2023, 10:27pm UTC](https://forum.qiime2.org/t/significative-adonis-test-but-no-significance-in-paired-adonis-test/27807 "2023-10-02T22:27:06Z")
Hi! Im comparing microbiota from different insect species, and i did by Permanova (or adonis) and i got a pvalue less than 0.05 but when i try to check which of them are different i got a P-paired value greather than 0.… --- ## [independent samples in alpha and beta diversity](https://forum.qiime2.org/t/independent-samples-in-alpha-and-beta-diversity/27509)
**Author:** [@elina2410](https://forum.qiime2.org/u/elina2410)\ **Replies:** 2\ **Last updated:** [August 31, 2023, 6:47am UTC](https://forum.qiime2.org/t/independent-samples-in-alpha-and-beta-diversity/27509 "2023-08-31T06:47:58Z")
Hello! I had an experiment with animals in which 6 groups were fed with addition of different compounds (study groups), and control group that got the same feed with no additives. Study design: Samples were taken from … --- ## [Statistical analyses for beta-rarefaction output](https://forum.qiime2.org/t/statistical-analyses-for-beta-rarefaction-output/27363)
**Author:** [@MarlydEMejia](https://forum.qiime2.org/u/MarlydEMejia)\ **Replies:** 1\ **Last updated:** [August 15, 2023, 4:24pm UTC](https://forum.qiime2.org/t/statistical-analyses-for-beta-rarefaction-output/27363 "2023-08-15T16:24:20Z")
Good afternoon! I realize there is a post similar to this Beta-rarefaction diversity matrix export or mean distance?, but was hoping bringing it up again to see if anything has been changed since or could be produced. I… --- ## [Alpha and Beta Diversity Plots](https://forum.qiime2.org/t/alpha-and-beta-diversity-plots/27320)
**Author:** [@ltunney](https://forum.qiime2.org/u/ltunney)\ **Replies:** 2\ **Last updated:** [August 7, 2023, 1:24pm UTC](https://forum.qiime2.org/t/alpha-and-beta-diversity-plots/27320 "2023-08-07T13:24:38Z")
Hello all! This is my first time looking at qiime2 data and I came out with two box plots with significant p-values. The first is a Shannon alpha plot and a Bray-Curtis Beta plot. How do I interpret these plots? I am con… --- ## [R squared on qiime diversity beta-group-significance](https://forum.qiime2.org/t/r-squared-on-qiime-diversity-beta-group-significance/27299)
**Author:** [@Edoardo\_Scali](https://forum.qiime2.org/u/Edoardo_Scali)\ **Replies:** 1\ **Last updated:** [August 4, 2023, 1:34pm UTC](https://forum.qiime2.org/t/r-squared-on-qiime-diversity-beta-group-significance/27299 "2023-08-04T13:34:12Z")
Hi everyone, I recieved a request from my PI and I would like to ask for assistance about this. Basically I would like to obtain R squared values for the diversity beta-group-significance analyses that I've done. I com… --- ## [Is the asv beta diversity plot on Emperor the same as if I made a PCoA plot myself?](https://forum.qiime2.org/t/is-the-asv-beta-diversity-plot-on-emperor-the-same-as-if-i-made-a-pcoa-plot-myself/26858)
**Author:** [@kkl45](https://forum.qiime2.org/u/kkl45)\ **Replies:** 4\ **Last updated:** [June 22, 2023, 6:44pm UTC](https://forum.qiime2.org/t/is-the-asv-beta-diversity-plot-on-emperor-the-same-as-if-i-made-a-pcoa-plot-myself/26858 "2023-06-22T18:44:44Z")
Using emperor, I have the output as below for unweighted unifrac. But when i manually use the unweighted unifrac distances and run a PCOA, i do not get the same plot. should they be equivalent? Edit: I think i fig… --- ## [Outliers in beta diversity analyses](https://forum.qiime2.org/t/outliers-in-beta-diversity-analyses/26813)
**Author:** [@Edoardo\_Scali](https://forum.qiime2.org/u/Edoardo_Scali)\ **Replies:** 4\ **Last updated:** [June 22, 2023, 6:38pm UTC](https://forum.qiime2.org/t/outliers-in-beta-diversity-analyses/26813 "2023-06-22T18:38:16Z")
Hi everyone, I have a question about the result that I've obtained running diversity analyses. I runned analyses with the "qiime diversity beta-group-significance" plugin for all the variables I have in my sample metada… --- ## [Alpha and Beta Diversity Explanations and Commands](https://forum.qiime2.org/t/alpha-and-beta-diversity-explanations-and-commands/2282)
**Author:** [@Stephanieorch](https://forum.qiime2.org/u/Stephanieorch)\ **Replies:** 6\ **Last updated:** [September 15, 2018, 5:06pm UTC](https://forum.qiime2.org/t/alpha-and-beta-diversity-explanations-and-commands/2282 "2018-09-15T17:06:14Z")
About the Alpha and Beta Diversity Analysis Tutorial This Alpha and Beta Diversity Community Tutorial (run using QIIME 2017.12) walks you through analyzing the alpha and beta diversity of a sample dataset. Below you will… --- ## [how to interpret group significance plot](https://forum.qiime2.org/t/how-to-interpret-group-significance-plot/24737)
**Author:** [@svbreqwaiu01](https://forum.qiime2.org/u/svbreqwaiu01)\ **Replies:** 1\ **Last updated:** [November 11, 2022, 1:37pm UTC](https://forum.qiime2.org/t/how-to-interpret-group-significance-plot/24737 "2022-11-11T13:37:22Z")
i have metter... i can\`t interpret group significance plot. what is more close to group 1?... group 2?? or group 3??? why 1 to 1 distance is highest among 3 groups?? i think 1 to 1 distance should be lowest… --- ## [meta analysis and weird looking emperor plot of beta-analysis](https://forum.qiime2.org/t/meta-analysis-and-weird-looking-emperor-plot-of-beta-analysis/23921)
**Author:** [@Jonathan](https://forum.qiime2.org/u/Jonathan)\ **Replies:** 8\ **Last updated:** [August 31, 2022, 10:41am UTC](https://forum.qiime2.org/t/meta-analysis-and-weird-looking-emperor-plot-of-beta-analysis/23921 "2022-08-31T10:41:42Z")
Hi all, I'm working with 16S data from several studies for meta-analysis. What I did is, import-cutadapt-denoise with dada2 (same primer pairs --\> same trim/trunc length, and used --p-max-ee-f,r for quality trim)-phylog… --- ## [Interpretation of Bray curtis box whisker plot](https://forum.qiime2.org/t/interpretation-of-bray-curtis-box-whisker-plot/23665)
**Author:** [@Shreya](https://forum.qiime2.org/u/Shreya)\ **Replies:** 2\ **Last updated:** [July 26, 2022, 1:27pm UTC](https://forum.qiime2.org/t/interpretation-of-bray-curtis-box-whisker-plot/23665 "2022-07-26T13:27:08Z")
Hello! I was wondering if anyone would be pleased to help me out for interpreting the Bray Curtis box whisker plot. Please elaborate the significance of the plot as well as the meaning of distance (n=66) as shown in the … --- ## [Beta diversity analysis p-value result interpretation](https://forum.qiime2.org/t/beta-diversity-analysis-p-value-result-interpretation/23214)
**Author:** [@Bowornpol\_Nuim](https://forum.qiime2.org/u/Bowornpol_Nuim)\ **Replies:** 1\ **Last updated:** [June 1, 2022, 5:23am UTC](https://forum.qiime2.org/t/beta-diversity-analysis-p-value-result-interpretation/23214 "2022-06-01T05:23:23Z")
I have struggled to interpret the p-value from permanova in beta diversity analysis. beta\_bray\_group\_significance\_new.qzv (514.5 KB) unweighted-unifrac-sig.qzv (707.8 KB) How can I interpret which group is significant… --- ## [ANCOM result interpretation?](https://forum.qiime2.org/t/ancom-result-interpretation/22841)
**Author:** [@Yavnika](https://forum.qiime2.org/u/Yavnika)\ **Replies:** 5\ **Last updated:** [May 27, 2022, 4:03pm UTC](https://forum.qiime2.org/t/ancom-result-interpretation/22841 "2022-05-27T16:03:14Z")
Hello, I'm new to the forum and trying to figure out a few things regarding abundance testing. I have 2 groups (test and control n=8, n=7 respectively) and I see significant differences between the 2 groups in terms of … --- ## [If the result of beta diversity in core-metrics-results was rarefacted?](https://forum.qiime2.org/t/if-the-result-of-beta-diversity-in-core-metrics-results-was-rarefacted/23170)
**Author:** [@YuZhang](https://forum.qiime2.org/u/YuZhang)\ **Replies:** 2\ **Last updated:** [May 25, 2022, 1:56pm UTC](https://forum.qiime2.org/t/if-the-result-of-beta-diversity-in-core-metrics-results-was-rarefacted/23170 "2022-05-25T13:56:56Z")
Dear all， I want to know if the result of beta diversity in core-metrics-results was rarefacted? --- ## [weighted vs unweighted unifrac?](https://forum.qiime2.org/t/weighted-vs-unweighted-unifrac/22904)
**Author:** [@Johanna\_Lisa\_Bosch](https://forum.qiime2.org/u/Johanna_Lisa_Bosch)\ **Replies:** 1\ **Last updated:** [April 27, 2022, 1:34pm UTC](https://forum.qiime2.org/t/weighted-vs-unweighted-unifrac/22904 "2022-04-27T13:34:50Z")
Hello! I am exploring the use of PCoA Unifrac plots in Qiime2 with some 16s amplicon data from fecal samples of different species While researching a bit about this I have come across a few people who say to use unweigh… --- ## [beta diversity PERMANOVA output](https://forum.qiime2.org/t/beta-diversity-permanova-output/22585)
**Author:** [@rr220](https://forum.qiime2.org/u/rr220)\ **Replies:** 2\ **Last updated:** [April 13, 2022, 11:44pm UTC](https://forum.qiime2.org/t/beta-diversity-permanova-output/22585 "2022-04-13T23:44:28Z")
Hello, I wanted to know how to obtain PERMANOVA output for beta diversity. In this regard I have following query: For running core metrics I ran following command: qiime diversity core-metrics-phylogenetic --i-phylo… --- ## [Collapsing feature table to a specific taxonomic rank before diversity analysis?](https://forum.qiime2.org/t/collapsing-feature-table-to-a-specific-taxonomic-rank-before-diversity-analysis/21806)
**Author:** [@pippo\_pippo](https://forum.qiime2.org/u/pippo_pippo)\ **Replies:** 4\ **Last updated:** [January 10, 2022, 12:37pm UTC](https://forum.qiime2.org/t/collapsing-feature-table-to-a-specific-taxonomic-rank-before-diversity-analysis/21806 "2022-01-10T12:37:21Z")
Hi there! I have a feature tabel from shotgun metagenomic sequencing which I produced with MetaPhlAn3. From there on, I use QIIME to calculate alpha diversity metrics. I am wondering if I should collapse my feature tab… --- ## [Interpretation of the PERMANOVA results](https://forum.qiime2.org/t/interpretation-of-the-permanova-results/20614)
**Author:** [@spencer886](https://forum.qiime2.org/u/spencer886)\ **Replies:** 3\ **Last updated:** [September 1, 2021, 7:08pm UTC](https://forum.qiime2.org/t/interpretation-of-the-permanova-results/20614 "2021-09-01T19:08:37Z")
Hi, I have followed the "Moving pictures" Tutorial to generate the PERMANOVA results using the beta-group-significance command. And I am confused about the PERMANOVA results: For example, for "Distances to gut", what… --- ## [Error in Beta Diversity - Pairwise sampling](https://forum.qiime2.org/t/error-in-beta-diversity-pairwise-sampling/7895)
**Author:** [@BeckyNesnevich](https://forum.qiime2.org/u/BeckyNesnevich)\ **Replies:** 1\ **Last updated:** [January 21, 2019, 9:24am UTC](https://forum.qiime2.org/t/error-in-beta-diversity-pairwise-sampling/7895 "2019-01-21T09:24:07Z")
Hello, I have been trying to run the beta-group-significance command using the option "--m-metadata-column Description" and have been getting this error message: "All values in the grouping vector are unique. This meth… --- ## [understanding bray curtis and Jaccard](https://forum.qiime2.org/t/understanding-bray-curtis-and-jaccard/19885)
**Author:** [@Sofita\_fuentes](https://forum.qiime2.org/u/Sofita_fuentes)\ **Replies:** 7\ **Last updated:** [June 16, 2021, 2:26am UTC](https://forum.qiime2.org/t/understanding-bray-curtis-and-jaccard/19885 "2021-06-16T02:26:27Z")
hi, i have an enormous question about how to interpret this results. i did a beta diversity analysis using jaccard and bray curtis metrics. According to the p-value, there is a significant difference bettwen my samples, … [Next page](https://forum.qiime2.org/tag/beta/87.md?match_all_tags=true&page=1&tags%5B%5D=beta)