# LEfSe **URL:** https://forum.biobakery.org/c/downstream-analysis-and-statistics/lefse/9.md [Latest](https://forum.biobakery.org/latest.md) · [Categories](https://forum.biobakery.org/categories.md) --- ## [About the Lefse category](https://forum.biobakery.org/t/about-the-lefse-category/23)
**Author:** [@sagunmaharjann](https://forum.biobakery.org/u/sagunmaharjann)\ **Replies:** 0
Name: LEfSe User manual || Tutorial Description: LEfSe (Linear discriminant analysis Effect Size) determines the features (organisms, clades, operational taxonomic units, genes, or functions) most likely to explain… --- ## [LEfSe analysis, plotting negative LDA score (log10)](https://forum.biobakery.org/t/lefse-analysis-plotting-negative-lda-score-log10/1294)
**Author:** [@Shaminur](https://forum.biobakery.org/u/Shaminur)\ **Replies:** 2\ **Last updated:** [February 19, 2026, 4:06pm UTC](https://forum.biobakery.org/t/lefse-analysis-plotting-negative-lda-score-log10/1294 "2026-02-19T16:06:59Z")
I want to plot LDA score with negative and positive like where should I need to change the parameter? --- ## [\[Huttenhower Lab Galaxy for LEfSE\]](https://forum.biobakery.org/t/huttenhower-lab-galaxy-for-lefse/8518)
**Author:** [@JayPark](https://forum.biobakery.org/u/JayPark)\ **Replies:** 1\ **Last updated:** [December 10, 2025, 4:59am UTC](https://forum.biobakery.org/t/huttenhower-lab-galaxy-for-lefse/8518 "2025-12-10T04:59:51Z")
While reading a paper, I attempted to perform an analysis using LEfSe (Galaxy Version 1.0) through the Galaxy tools. However, even after formatting my files properly and repeatedly uploading them before execution, I con… --- ## [Trying to format LEfSe](https://forum.biobakery.org/t/trying-to-format-lefse/8521)
**Author:** [@Aris](https://forum.biobakery.org/u/Aris)\ **Replies:** 0\ **Last updated:** [September 24, 2025, 8:16pm UTC](https://forum.biobakery.org/t/trying-to-format-lefse/8521 "2025-09-24T20:16:42Z")
This is my first time using Galaxy LEfSe, and I appear to be having difficulty trying to run my data set. The first few participant data points are Sample\_ID DOM00003 DOM00004 DOM00006 HIV\_Status HI HI HI CD4\_… --- ## [No taxa labels after lefse\_plot\_cladogram.py](https://forum.biobakery.org/t/no-taxa-labels-after-lefse-plot-cladogram-py/5868)
**Author:** [@clidia23](https://forum.biobakery.org/u/clidia23)\ **Replies:** 4\ **Last updated:** [August 26, 2025, 9:06am UTC](https://forum.biobakery.org/t/no-taxa-labels-after-lefse-plot-cladogram-py/5868 "2025-08-26T09:06:46Z")
Hi, I couldnt get any taxa labels after generating cladogram via lefse\_plot\_cladogram.py within conda environment. I also check all the usage options, however still no taxa labels at right side. There is also no acc… --- ## [Missing Legend in Lefse Cladogram Plot Generated via Conda Environment](https://forum.biobakery.org/t/missing-legend-in-lefse-cladogram-plot-generated-via-conda-environment/8237)
**Author:** [@TKurakawa](https://forum.biobakery.org/u/TKurakawa)\ **Replies:** 0\ **Last updated:** [July 7, 2025, 2:19am UTC](https://forum.biobakery.org/t/missing-legend-in-lefse-cladogram-plot-generated-via-conda-environment/8237 "2025-07-07T02:19:38Z")
Hello. I am currently using lefse\_plot\_cladogram.py within a conda environment to generate cladogram plots from LEfSe output files. While the cladogram images are generated successfully, the group/class legends do not a… --- ## [LEfSe issues and errors](https://forum.biobakery.org/t/lefse-issues-and-errors/5397)
**Author:** [@garretta](https://forum.biobakery.org/u/garretta)\ **Replies:** 39\ **Last updated:** [March 13, 2025, 7:50pm UTC](https://forum.biobakery.org/t/lefse-issues-and-errors/5397 "2025-03-13T19:50:32Z")
Hi. I have been using LEfSe in the past and was successfully able to run the full pipeline with the Galaxy LEfSe tool. Now when I am trying to run the pipeline using new tabular files (I believe to be formatted correctly… --- ## [Need Help with Galaxy LEfSe LDA Step Error](https://forum.biobakery.org/t/need-help-with-galaxy-lefse-lda-step-error/7804)
**Author:** [@jeylee](https://forum.biobakery.org/u/jeylee)\ **Replies:** 1\ **Last updated:** [February 27, 2025, 11:53pm UTC](https://forum.biobakery.org/t/need-help-with-galaxy-lefse-lda-step-error/7804 "2025-02-27T23:53:07Z")
Here’s the revised version with improved grammar and clarity: Hi, I haven’t used Galaxy LEfSe analysis for a while, and I recently tried to use it again. However, I’m unable to proceed beyond the LDA Effect Size step. … --- ## [How to include other subclades/taxa in the resulting plot?](https://forum.biobakery.org/t/how-to-include-other-subclades-taxa-in-the-resulting-plot/7777)
**Author:** [@John\_Kim\_Aligato](https://forum.biobakery.org/u/John_Kim_Aligato)\ **Replies:** 1\ **Last updated:** [February 18, 2025, 7:54pm UTC](https://forum.biobakery.org/t/how-to-include-other-subclades-taxa-in-the-resulting-plot/7777 "2025-02-18T19:54:54Z")
I used LEfSe v1.1.2 and processed my input ASV table using dokdo. Hi LEfSe community! I would like to ask a question about the lefse\_plot\_res.py wrapper script. All of other processes before that ran smoothly. In my cas… --- ## [Print all groups that satisfy the p-value cutoff in .res file (not just top lda group)](https://forum.biobakery.org/t/print-all-groups-that-satisfy-the-p-value-cutoff-in-res-file-not-just-top-lda-group/7610)
**Author:** [@jihyunchun](https://forum.biobakery.org/u/jihyunchun)\ **Replies:** 0\ **Last updated:** [November 27, 2024, 2:23am UTC](https://forum.biobakery.org/t/print-all-groups-that-satisfy-the-p-value-cutoff-in-res-file-not-just-top-lda-group/7610 "2024-11-27T02:23:15Z")
Hi, I’m using LEfSe 1.1.01 on Linux (Ubuntu). I have five groups in my data, and I want the significantly abundant taxa to be identified for each group. I’ve noticed that the results differ depending on the number of g… --- ## [Different results with LEfSe on between Galaxy and Conda](https://forum.biobakery.org/t/different-results-with-lefse-on-between-galaxy-and-conda/5929)
**Author:** [@Sarasa](https://forum.biobakery.org/u/Sarasa)\ **Replies:** 3\ **Last updated:** [November 18, 2024, 8:12am UTC](https://forum.biobakery.org/t/different-results-with-lefse-on-between-galaxy-and-conda/5929 "2024-11-18T08:12:57Z")
Hi everyone, Why did I see the different results on between galaxy platform and local environment (mac, conda)? During galaxy was down, I used Lefse with local conda environment in mac. The same data set was computed … --- ## [Exporting Results/LDA scores to .tsv with conda?](https://forum.biobakery.org/t/exporting-results-lda-scores-to-tsv-with-conda/6407)
**Author:** [@tubber4](https://forum.biobakery.org/u/tubber4)\ **Replies:** 3\ **Last updated:** [November 18, 2024, 7:46am UTC](https://forum.biobakery.org/t/exporting-results-lda-scores-to-tsv-with-conda/6407 "2024-11-18T07:46:55Z")
Hi, I am new LEfSe and bioinformatics in general, but I have successfully run the analysis with conda. However, looking through the tutorials (apologies if I missed it) I couldn’t find a way to see a table with taxa an… --- ## [Lefse\_bug LDA run had a bug](https://forum.biobakery.org/t/lefse-bug-lda-run-had-a-bug/7167)
**Author:** [@Phyllis](https://forum.biobakery.org/u/Phyllis)\ **Replies:** 2\ **Last updated:** [November 12, 2024, 4:39am UTC](https://forum.biobakery.org/t/lefse-bug-lda-run-had-a-bug/7167 "2024-11-12T04:39:58Z")
Hi, I have been using LEfSe in the past and was successfully able to run the full pipeline with the Galaxy LEfSe tool. Now even with old ones that successfully worked in the past I have a problem with B step of Lefse mo… --- ## [Error in when running lefse on Galaxy in step B (LDA effect size)](https://forum.biobakery.org/t/error-in-when-running-lefse-on-galaxy-in-step-b-lda-effect-size/7439)
**Author:** [@thilini](https://forum.biobakery.org/u/thilini)\ **Replies:** 0\ **Last updated:** [September 11, 2024, 12:45pm UTC](https://forum.biobakery.org/t/error-in-when-running-lefse-on-galaxy-in-step-b-lda-effect-size/7439 "2024-09-11T12:45:04Z")
HI, I am running the demo dataset but get the following error for step B on Galaxy. Number of significantly discriminative features: 8 ( 131 ) before internal wilcoxon Traceback (most recent call last): File “/galaxy\_… --- ## [Number of significantly discriminative features: 311 ( 311 ) before internal wilcoxon](https://forum.biobakery.org/t/number-of-significantly-discriminative-features-311-311-before-internal-wilcoxon/7367)
**Author:** [@rocilia](https://forum.biobakery.org/u/rocilia)\ **Replies:** 0\ **Last updated:** [August 14, 2024, 6:07am UTC](https://forum.biobakery.org/t/number-of-significantly-discriminative-features-311-311-before-internal-wilcoxon/7367 "2024-08-14T06:07:17Z")
Hi! I meet this error when running LEfSe (http://galaxy.biobakery.org/). Step A) runs well but an error is reported in Step B). An error occurred with this dataset: Number of significantly discriminative features: 2… --- ## [Number of significantly discriminative features: 8 ( 131 ) before internal wilcoxon](https://forum.biobakery.org/t/number-of-significantly-discriminative-features-8-131-before-internal-wilcoxon/7284)
**Author:** [@JUAN\_VICENTE\_VALOR](https://forum.biobakery.org/u/JUAN_VICENTE_VALOR)\ **Replies:** 1\ **Last updated:** [August 13, 2024, 3:26pm UTC](https://forum.biobakery.org/t/number-of-significantly-discriminative-features-8-131-before-internal-wilcoxon/7284 "2024-08-13T15:26:34Z")
Hi! I am trying to run the example you have on the web page. http://galaxy.biobakery.org/ Sample\_LefSe\_Input --\>hmp\_aerobiosis\_small However I am retrieving this error in the step of running the LEfSe, which I do not … --- ## [Lefse problem with plotting](https://forum.biobakery.org/t/lefse-problem-with-plotting/5574)
**Author:** [@ShonB07](https://forum.biobakery.org/u/ShonB07)\ **Replies:** 1\ **Last updated:** [July 24, 2024, 5:46am UTC](https://forum.biobakery.org/t/lefse-problem-with-plotting/5574 "2024-07-24T05:46:26Z")
Trying to analyze my own data on Lefse on Galaxy and getting error on the third step, in term during plotting Lefse results. Could someone help me to manage this error: The image “http://huttenhower.sph.harvard.edu/galax… --- ## [Lefse error :- No differentially abundant features](https://forum.biobakery.org/t/lefse-error-no-differentially-abundant-features/7310)
**Author:** [@ayush\_jain](https://forum.biobakery.org/u/ayush_jain)\ **Replies:** 0\ **Last updated:** [July 24, 2024, 5:43am UTC](https://forum.biobakery.org/t/lefse-error-no-differentially-abundant-features/7310 "2024-07-24T05:43:46Z")
Hi, I’m trying to go through your LEfSe platform on galaxy and I keep getting an error at the C) step. This is the message I get: No differentially abundant features found in /home/usr/local/galaxy-dist/database/files/… --- ## [rpy2.rinterface.RRuntimeError](https://forum.biobakery.org/t/rpy2-rinterface-rruntimeerror/7308)
**Author:** [@chengyi](https://forum.biobakery.org/u/chengyi)\ **Replies:** 0\ **Last updated:** [July 23, 2024, 9:18am UTC](https://forum.biobakery.org/t/rpy2-rinterface-rruntimeerror/7308 "2024-07-23T09:18:04Z")
I am analysis with microbial data when I run run\_lefse.py data.in data.res it has following error: /home/linuxbrew/.linuxbrew/Cellar/lefse/1.0.0-dev-e3cabe9/libexec/lib/python2.7/site-packages/rpy2/robjects/functions.… --- ## [Lefse installation](https://forum.biobakery.org/t/lefse-installation/7237)
**Author:** [@Shwetha\_Kumar](https://forum.biobakery.org/u/Shwetha_Kumar)\ **Replies:** 2\ **Last updated:** [July 18, 2024, 7:23pm UTC](https://forum.biobakery.org/t/lefse-installation/7237 "2024-07-18T19:23:35Z")
What is the best way to install? I have been trying since months but I need to get all the tools (from biobakery) installed and most of them are not straightforward. The galaxy is not accessible. I am at my wits end. Thi… --- ## [LEfSe for humann3](https://forum.biobakery.org/t/lefse-for-humann3/6629)
**Author:** [@Dhananjai\_Mp](https://forum.biobakery.org/u/Dhananjai_Mp)\ **Replies:** 2\ **Last updated:** [June 5, 2024, 5:45pm UTC](https://forum.biobakery.org/t/lefse-for-humann3/6629 "2024-06-05T17:45:30Z")
Hi. I have pathways result from Humann3 that I would like to perform stat and visualization. I have one metadata with categorical variables. Can I use LEfSe for this? Or should I go with Maaslin? Please provide your feed… --- ## [TypeError: slice indices must be integers or None or have an \_\_index\_\_ method](https://forum.biobakery.org/t/typeerror-slice-indices-must-be-integers-or-none-or-have-an-index-method/6891)
**Author:** [@toba1](https://forum.biobakery.org/u/toba1)\ **Replies:** 1\ **Last updated:** [May 30, 2024, 1:02pm UTC](https://forum.biobakery.org/t/typeerror-slice-indices-must-be-integers-or-none-or-have-an-index-method/6891 "2024-05-30T13:02:55Z")
Hi everyone! I would like to lefse figure, but I got that error. (lefse) eb-pth-j4yxwm37:exported-featureca-table toba1$ lefse\_plot\_res.py biome.res biome.png Traceback (most recent call last): File “/Users/miniconda… --- ## [Problem using LEfSe on Galaxy - can't format data for LEfSe](https://forum.biobakery.org/t/problem-using-lefse-on-galaxy-cant-format-data-for-lefse/373)
**Author:** [@Alibba](https://forum.biobakery.org/u/Alibba)\ **Replies:** 7\ **Last updated:** [May 3, 2024, 8:55pm UTC](https://forum.biobakery.org/t/problem-using-lefse-on-galaxy-cant-format-data-for-lefse/373 "2024-05-03T20:55:40Z")
I am new to LEfSe and am trying to do a LEfSe analysis for a microbial dataset I have, and I seem to be having difficulty getting LEfSe to read in my file (can’t seem to attach as a new user) and format it for analysis. … --- ## [LEfSe downstream processing issue: LDA tool not showing any difference between the classes](https://forum.biobakery.org/t/lefse-downstream-processing-issue-lda-tool-not-showing-any-difference-between-the-classes/6972)
**Author:** [@Natasha](https://forum.biobakery.org/u/Natasha)\ **Replies:** 0\ **Last updated:** [April 26, 2024, 6:29am UTC](https://forum.biobakery.org/t/lefse-downstream-processing-issue-lda-tool-not-showing-any-difference-between-the-classes/6972 "2024-04-26T06:29:38Z")
The LDA effect size tool is giving me the following error for my dataset. I have 3 groups that i want to compare and a total of 105 features. R\[write to console\]: Error in lda.default(x, grouping, …) : variables 1 … --- ## [Unable to access the Galaxy module of lefse](https://forum.biobakery.org/t/unable-to-access-the-galaxy-module-of-lefse/5859)
**Author:** [@Saira](https://forum.biobakery.org/u/Saira)\ **Replies:** 34\ **Last updated:** [April 17, 2024, 8:47pm UTC](https://forum.biobakery.org/t/unable-to-access-the-galaxy-module-of-lefse/5859 "2024-04-17T20:47:58Z")
Hi, I can’t access the Galaxy module of the lefse, is there any problem with the server or what’s the matter?. Please can anybody help me regarding this. Thanks --- ## [Tutorial: AttributeError: 'NoneType' object has no attribute 'rownames'AttributeError: 'NoneType' object has no attribute 'rownames'](https://forum.biobakery.org/t/tutorial-attributeerror-nonetype-object-has-no-attribute-rownamesattributeerror-nonetype-object-has-no-attribute-rownames/5466)
**Author:** [@Taha\_Zakariya](https://forum.biobakery.org/u/Taha_Zakariya)\ **Replies:** 2\ **Last updated:** [April 11, 2024, 5:36pm UTC](https://forum.biobakery.org/t/tutorial-attributeerror-nonetype-object-has-no-attribute-rownamesattributeerror-nonetype-object-has-no-attribute-rownames/5466 "2024-04-11T17:36:49Z")
Hello, It’s my first time trying lefse through CLI, but i get the following error when I run the tutorial pipeline, in the lefse\_run step, here’s the detailed error: (test) MacBook-Pro-de-Taha:Desktop tahazakariya$ lef… --- ## [LEfSe: one-tailed or two-tailed p-values?](https://forum.biobakery.org/t/lefse-one-tailed-or-two-tailed-p-values/6802)
**Author:** [@Hasti\_A](https://forum.biobakery.org/u/Hasti_A)\ **Replies:** 0\ **Last updated:** [March 17, 2024, 8:04pm UTC](https://forum.biobakery.org/t/lefse-one-tailed-or-two-tailed-p-values/6802 "2024-03-17T20:04:37Z")
Hello! I’ve found LEfSe to be quite useful for my microbiome analysis. Just out of curiosity, are the p-values produced from LDA one-tailed or two-tailed? Thanks, in advance! --- ## [Format input file for Lefse](https://forum.biobakery.org/t/format-input-file-for-lefse/5518)
**Author:** [@Josias](https://forum.biobakery.org/u/Josias)\ **Replies:** 33\ **Last updated:** [March 7, 2024, 7:32pm UTC](https://forum.biobakery.org/t/format-input-file-for-lefse/5518 "2024-03-07T19:32:15Z")
Hi, Even using the website suggested input file, I was unable to pass from the format step: Error: error An error occurred with this dataset: Traceback (most recent call last): File “/usr/bin/lefse\_format\_input.py”,… --- ## [Unnable to acces galaxy.biobakery.org - Proxy Error](https://forum.biobakery.org/t/unnable-to-acces-galaxy-biobakery-org-proxy-error/6373)
**Author:** [@amtoscani](https://forum.biobakery.org/u/amtoscani)\ **Replies:** 6\ **Last updated:** [March 6, 2024, 12:54am UTC](https://forum.biobakery.org/t/unnable-to-acces-galaxy-biobakery-org-proxy-error/6373 "2024-03-06T00:54:13Z")
Hello, Since December 20th 2023 I am unnable to acces galaxy.biobakery.org, in order to use LEfSe workflow. The following message comes to screen: Proxy Error The proxy server received an invalid response from an upstr… --- ## [Does a negative LDA score mean the abundance is less?](https://forum.biobakery.org/t/does-a-negative-lda-score-mean-the-abundance-is-less/6738)
**Author:** [@Priscy\_William](https://forum.biobakery.org/u/Priscy_William)\ **Replies:** 0\ **Last updated:** [March 1, 2024, 6:54am UTC](https://forum.biobakery.org/t/does-a-negative-lda-score-mean-the-abundance-is-less/6738 "2024-03-01T06:54:16Z")
Hi I did a Lefse analysis which showed both positive and negative LDA scores. How must I take the negative LDA score. Does a negative LDA represent lower abundance and positive LDA a higher abundance ? What does the n… [Next page](https://forum.biobakery.org/c/downstream-analysis-and-statistics/lefse/9.md?page=1)