# GraPhlAn **URL:** https://forum.biobakery.org/c/infrastructure-and-utilities/graphlan/17.md [Latest](https://forum.biobakery.org/latest.md) · [Categories](https://forum.biobakery.org/categories.md) --- ## [About the GraPhlAn category](https://forum.biobakery.org/t/about-the-graphlan-category/31)
**Author:** [@sagunmaharjann](https://forum.biobakery.org/u/sagunmaharjann)\ **Replies:** 0
Name: GraPhlAn User manual || Tutorial Description: GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees. GraPhlAn focuses on concise, integrative, inf… --- ## [Annotation with phyla data](https://forum.biobakery.org/t/annotation-with-phyla-data/8046)
**Author:** [@apoosakkannu](https://forum.biobakery.org/u/apoosakkannu)\ **Replies:** 0\ **Last updated:** [May 8, 2025, 11:55am UTC](https://forum.biobakery.org/t/annotation-with-phyla-data/8046 "2025-05-08T11:55:37Z")
Hello, I have generated a tree of metagenome assembled genomes with latest Phylophlan software. I am interested in adding taxonomy data in the tree with different colours and also if possible some other details such as h… --- ## [Graphlan error: Classes not implemented](https://forum.biobakery.org/t/graphlan-error-classes-not-implemented/7578)
**Author:** [@KaushikRaman](https://forum.biobakery.org/u/KaushikRaman)\ **Replies:** 4\ **Last updated:** [November 25, 2024, 7:32pm UTC](https://forum.biobakery.org/t/graphlan-error-classes-not-implemented/7578 "2024-11-25T19:32:10Z")
Issue with GraPhlAn Annotations: I have been using GraPhlAn (version 1.1.4) to generate a phylogenetic figure for a project involving 9907 samples. The goal is to annotate each clade and add ring colors based on specifi… --- ## [Installation graphlan](https://forum.biobakery.org/t/installation-graphlan/7236)
**Author:** [@Shwetha\_Kumar](https://forum.biobakery.org/u/Shwetha_Kumar)\ **Replies:** 4\ **Last updated:** [August 17, 2024, 4:42pm UTC](https://forum.biobakery.org/t/installation-graphlan/7236 "2024-08-17T16:42:07Z")
I am not sure this has been quite answered in the previous posts as well. I have this issue with installing graphaln. I get this error. include/python3.12 -c Bio/triemodule.c -o build/temp.macosx-10.9-x86\_64-cpython-312… --- ## [Failed building wheel for biopython](https://forum.biobakery.org/t/failed-building-wheel-for-biopython/6149)
**Author:** [@cchin](https://forum.biobakery.org/u/cchin)\ **Replies:** 2\ **Last updated:** [July 5, 2024, 6:42pm UTC](https://forum.biobakery.org/t/failed-building-wheel-for-biopython/6149 "2024-07-05T18:42:57Z")
Hi I am trying to install Graphlan on a Mac. I have chance the shell to Bash, running on M2, Sonoma 14.0, and python 3. However I am getting the following error and hoping someone can help me. Seems to be a problem wit… --- ## [Can't change annotation colors on graphlan cladogram](https://forum.biobakery.org/t/cant-change-annotation-colors-on-graphlan-cladogram/7185)
**Author:** [@rachel](https://forum.biobakery.org/u/rachel)\ **Replies:** 0\ **Last updated:** [June 21, 2024, 10:09pm UTC](https://forum.biobakery.org/t/cant-change-annotation-colors-on-graphlan-cladogram/7185 "2024-06-21T22:09:59Z")
Hi, I’m very new to using graphlan. I have a cladogram that was generated with lefse using the Galaxy website. I’ve been asked to format this cladogram a bit differently using graphlan. I’ve installed both export2graphla… --- ## [AttributeError: 'Clade' object has no attribute 'fc'](https://forum.biobakery.org/t/attributeerror-clade-object-has-no-attribute-fc/6390)
**Author:** [@burdungy](https://forum.biobakery.org/u/burdungy)\ **Replies:** 0\ **Last updated:** [January 2, 2024, 8:21pm UTC](https://forum.biobakery.org/t/attributeerror-clade-object-has-no-attribute-fc/6390 "2024-01-02T20:21:20Z")
When I try to visualize my phylogenetic tree with annotation file, I got this error. Did anyone encounter before? Traceback (most recent call last): File “/mnt/rstor/CSE\_CSDS\_VXC204/rxl761/miniconda/envs/graphlan/bin/g… --- ## [Some annotations do not show in my output tree](https://forum.biobakery.org/t/some-annotations-do-not-show-in-my-output-tree/6312)
**Author:** [@burdungy](https://forum.biobakery.org/u/burdungy)\ **Replies:** 0\ **Last updated:** [December 13, 2023, 4:42pm UTC](https://forum.biobakery.org/t/some-annotations-do-not-show-in-my-output-tree/6312 "2023-12-13T16:42:53Z")
Hi, I just create a annotation file and a tree file, but all the tip annotation can be shown and all the internal annotation can not be shown, here are my tree file and annotation file, can you help me check them? new\_… --- ## [Global tree options annotating legend instead of tree nodes](https://forum.biobakery.org/t/global-tree-options-annotating-legend-instead-of-tree-nodes/4319)
**Author:** [@tbranck](https://forum.biobakery.org/u/tbranck)\ **Replies:** 1\ **Last updated:** [December 13, 2023, 4:18pm UTC](https://forum.biobakery.org/t/global-tree-options-annotating-legend-instead-of-tree-nodes/4319 "2023-12-13T16:18:34Z")
Hello, I’ve set up my annotation file to note the color, shape and size of the nodes, but the parameters are annotating the tree legend instead of the tree itself. Input files (tree, annotation file) and output tree are… --- ## [Annotation file options not generated in the output image](https://forum.biobakery.org/t/annotation-file-options-not-generated-in-the-output-image/6147)
**Author:** [@Stanlley\_Titus](https://forum.biobakery.org/u/Stanlley_Titus)\ **Replies:** 0\ **Last updated:** [October 30, 2023, 8:51am UTC](https://forum.biobakery.org/t/annotation-file-options-not-generated-in-the-output-image/6147 "2023-10-30T08:51:57Z")
Hi, I have a tree file in Newick format for which I am trying to use Graphlan to annotate it with colors and other options. I created the annotation file but the colors are not displayed in the output image. Only the gl… --- ## [Pie charts in nodes and branches](https://forum.biobakery.org/t/pie-charts-in-nodes-and-branches/5804)
**Author:** [@sdgamboa](https://forum.biobakery.org/u/sdgamboa)\ **Replies:** 0\ **Last updated:** [August 23, 2023, 9:48pm UTC](https://forum.biobakery.org/t/pie-charts-in-nodes-and-branches/5804 "2023-08-23T21:48:20Z")
Is there a way to display pie charts in internal nodes, leaves, and branches? --- ## [Ring depicting relative abundance by sample metadata](https://forum.biobakery.org/t/ring-depicting-relative-abundance-by-sample-metadata/5564)
**Author:** [@zmcadams](https://forum.biobakery.org/u/zmcadams)\ **Replies:** 0\ **Last updated:** [June 30, 2023, 3:11pm UTC](https://forum.biobakery.org/t/ring-depicting-relative-abundance-by-sample-metadata/5564 "2023-06-30T15:11:49Z")
Hi, Is there anyway to depict relative abundance within a sample category in a ring? I’m trying to emulate what can be done with EMPress as seen here. Thanks! --- ## [Classes not implemented for external annotations](https://forum.biobakery.org/t/classes-not-implemented-for-external-annotations/5353)
**Author:** [@Theo\_Allnutt](https://forum.biobakery.org/u/Theo_Allnutt)\ **Replies:** 1\ **Last updated:** [June 5, 2023, 3:39am UTC](https://forum.biobakery.org/t/classes-not-implemented-for-external-annotations/5353 "2023-06-05T03:39:28Z")
Hi, getting same error as previous post which was not resolved. Can’t see anything wrong with annotation file. Thanks. graphlan\_annotate.py --annot data.txt family\_pruned.tree tree.xml family\_pruned.tree.txt (8.5 KB) … --- ## [Poor annotation alignment and strange branches](https://forum.biobakery.org/t/poor-annotation-alignment-and-strange-branches/5381)
**Author:** [@Theo\_Allnutt](https://forum.biobakery.org/u/Theo_Allnutt)\ **Replies:** 0\ **Last updated:** [June 5, 2023, 3:38am UTC](https://forum.biobakery.org/t/poor-annotation-alignment-and-strange-branches/5381 "2023-06-05T03:38:18Z")
See attached image. The labels and bars are not well aligned. Also some long internal branches run diagonally instead of radially. Thanks. --- ## [Graphphlan label](https://forum.biobakery.org/t/graphphlan-label/3016)
**Author:** [@Unaimend](https://forum.biobakery.org/u/Unaimend)\ **Replies:** 2\ **Last updated:** [May 16, 2023, 5:13am UTC](https://forum.biobakery.org/t/graphphlan-label/3016 "2023-05-16T05:13:11Z")
Is there some way to assign a label to an outer ring? I know I can assign labels to the taxonomic data with internal\_label and another question is there a way to include labels for every leaf? I was able to include them\[… --- ## [ZeroDivisionError in GraPhlAn](https://forum.biobakery.org/t/zerodivisionerror-in-graphlan/5235)
**Author:** [@Alberto\_Pascale](https://forum.biobakery.org/u/Alberto_Pascale)\ **Replies:** 0\ **Last updated:** [May 4, 2023, 8:59am UTC](https://forum.biobakery.org/t/zerodivisionerror-in-graphlan/5235 "2023-05-04T08:59:46Z")
Hi, am getting this following error when running GraPhlAn 1.1.3 File "/Users/alb/anaconda3/envs/graphlan/bin/graphlan.py", line 79, in \ reorder\_tree=args\['avoid\_reordering'\]) File "/Users/alb/anaconda3/env… --- ## [Cannot install GraPhlAn](https://forum.biobakery.org/t/cannot-install-graphlan/4792)
**Author:** [@sasakitomiyano](https://forum.biobakery.org/u/sasakitomiyano)\ **Replies:** 2\ **Last updated:** [February 14, 2023, 12:49am UTC](https://forum.biobakery.org/t/cannot-install-graphlan/4792 "2023-02-14T00:49:06Z")
I am having trouble trying to install GraPhlAn using ubuntu. I have already created a separate environment. I don’t understand why it cannot find matplotlib. (graphlan) sasaki@LAPTOP-9GD:~$ mamba install -c bioconda -c … --- ## [Plot\_tree\_graphlan.py error!](https://forum.biobakery.org/t/plot-tree-graphlan-py-error/666)
**Author:** [@Bahtiyar\_Yilmaz](https://forum.biobakery.org/u/Bahtiyar_Yilmaz)\ **Replies:** 2\ **Last updated:** [October 20, 2022, 7:44am UTC](https://forum.biobakery.org/t/plot-tree-graphlan-py-error/666 "2022-10-20T07:44:48Z")
Dear all, I tried to follow up the tutorial in Home · biobakery/MetaPhlAn Wiki · GitHub after installing with conda and tried to plot in graphlan here is what I run: plot\_tree\_graphlan.py --ifn\_tree output/RAxML\_bestTr… --- ## [Metaphlan3 to graphlan](https://forum.biobakery.org/t/metaphlan3-to-graphlan/3845)
**Author:** [@Mad\_Cat](https://forum.biobakery.org/u/Mad_Cat)\ **Replies:** 0\ **Last updated:** [July 17, 2022, 3:49pm UTC](https://forum.biobakery.org/t/metaphlan3-to-graphlan/3845 "2022-07-17T15:49:56Z")
Hi! I wanted to ask for help with Galaxy module (Galaxy) of GraPhlAn. When trying to Annotate tree on a file (guide.txt) taken from here (graphlan · biobakery/biobakery Wiki · GitHub), the following error is presented. … --- ## [Ring titles location relative to the tree](https://forum.biobakery.org/t/ring-titles-location-relative-to-the-tree/3703)
**Author:** [@saar](https://forum.biobakery.org/u/saar)\ **Replies:** 0\ **Last updated:** [June 9, 2022, 1:00pm UTC](https://forum.biobakery.org/t/ring-titles-location-relative-to-the-tree/3703 "2022-06-09T13:00:49Z")
when plotting a tree with rings and corresponding titles, is it possible to set which leaf/species would be the first one after the titles? Thanks! --- ## [Order legend with Graphlan](https://forum.biobakery.org/t/order-legend-with-graphlan/3461)
**Author:** [@hariszaf](https://forum.biobakery.org/u/hariszaf)\ **Replies:** 0\ **Last updated:** [April 16, 2022, 6:22pm UTC](https://forum.biobakery.org/t/order-legend-with-graphlan/3461 "2022-04-16T18:22:00Z")
Hello there. I would like to ask you whether I could order the legend of my taxonomies in Graphlan not alphabetically but in the order they appear on the tree (clockwise). Thank you for your time and help in advance. … --- ## [Export2graphlan - how to incorporate metadata as ring annotations?](https://forum.biobakery.org/t/export2graphlan-how-to-incorporate-metadata-as-ring-annotations/1900)
**Author:** [@acvill](https://forum.biobakery.org/u/acvill)\ **Replies:** 2\ **Last updated:** [February 15, 2022, 2:17pm UTC](https://forum.biobakery.org/t/export2graphlan-how-to-incorporate-metadata-as-ring-annotations/1900 "2022-02-15T14:17:10Z")
Thank you for providing and maintaining this great suite of tools. I have been following the guide here to create hclust2 heatmaps and GraPhlAn cladograms for visualization of MetaPhlAn2 profiles. My GraPhlAn workflow … --- ## [Newick Tree Format](https://forum.biobakery.org/t/newick-tree-format/3022)
**Author:** [@Unaimend](https://forum.biobakery.org/u/Unaimend)\ **Replies:** 1\ **Last updated:** [February 4, 2022, 3:18pm UTC](https://forum.biobakery.org/t/newick-tree-format/3022 "2022-02-04T15:18:05Z")
How does a tree in Newick format have to look like so I can color with an annotation file --- ## [Rotated Leaf Labels](https://forum.biobakery.org/t/rotated-leaf-labels/3057)
**Author:** [@MichaWeb75](https://forum.biobakery.org/u/MichaWeb75)\ **Replies:** 0\ **Last updated:** [January 31, 2022, 12:10pm UTC](https://forum.biobakery.org/t/rotated-leaf-labels/3057 "2022-01-31T12:10:27Z")
I aimed to annotate each leaf in a Graphlan phylogenetic tree with a rotated label using the attribute annotation\_rotation 90. There is still a deviation from the position of the leaf label and the clade. Do you know a … --- ## [Graphlan heatmap legend](https://forum.biobakery.org/t/graphlan-heatmap-legend/3056)
**Author:** [@MichaWeb75](https://forum.biobakery.org/u/MichaWeb75)\ **Replies:** 0\ **Last updated:** [January 31, 2022, 10:54am UTC](https://forum.biobakery.org/t/graphlan-heatmap-legend/3056 "2022-01-31T10:54:03Z")
Dear all, I am wondering how to add a heatmap legend scale, similarily to functions such as R heatmap.2. For example in the tutorial there are two outer heatmap rings, colored with ring\_alpha Bacillaceae.Bacillus.Blic… --- ## [Plot Clade Markers inside separator](https://forum.biobakery.org/t/plot-clade-markers-inside-separator/3020)
**Author:** [@MichaWeb75](https://forum.biobakery.org/u/MichaWeb75)\ **Replies:** 0\ **Last updated:** [January 19, 2022, 10:45am UTC](https://forum.biobakery.org/t/plot-clade-markers-inside-separator/3020 "2022-01-19T10:45:35Z")
Hi, I am wondering how to plot rotated clade markers with annotation\_rotation (labels) between the tree and the first ring, in such a way that they are still covered by the background color. I tried to adjust annotation… --- ## [How to create Annotation file](https://forum.biobakery.org/t/how-to-create-annotation-file/626)
**Author:** [@Suwitchaya](https://forum.biobakery.org/u/Suwitchaya)\ **Replies:** 2\ **Last updated:** [November 10, 2021, 1:53pm UTC](https://forum.biobakery.org/t/how-to-create-annotation-file/626 "2021-11-10T13:53:15Z")
Now, I analyte gut microbiome by using qiime2 pipeline. So, I interest to present data in circular representations of taxonomic and phylogenetic trees by using GraPhlAn but I have no idea how to create annotation file l… --- ## [Error when running export2graphlan.py](https://forum.biobakery.org/t/error-when-running-export2graphlan-py/1103)
**Author:** [@elenu](https://forum.biobakery.org/u/elenu)\ **Replies:** 4\ **Last updated:** [September 11, 2021, 9:00am UTC](https://forum.biobakery.org/t/error-when-running-export2graphlan-py/1103 "2021-09-11T09:00:31Z")
Dear all, I tried to run this code from the tutorial: $ export2graphlan.py --skip\_rows 1,2 -i merged\_abundance\_table.txt --tree merged\_abundance.tree.txt --annotation merged\_abundance.annot.txt --most\_abundant 100 --ab… --- ## [Nodes appear aligned](https://forum.biobakery.org/t/nodes-appear-aligned/2549)
**Author:** [@elenu](https://forum.biobakery.org/u/elenu)\ **Replies:** 1\ **Last updated:** [September 10, 2021, 3:56pm UTC](https://forum.biobakery.org/t/nodes-appear-aligned/2549 "2021-09-10T15:56:20Z")
Hi, I have tried to run the example showed in the Wiki but the outcome in the first plot was different: Due to I have copied and pasted the same codes I do not know what happened. Thank you. Elena --- ## [Graphlan tree file](https://forum.biobakery.org/t/graphlan-tree-file/2558)
**Author:** [@Amina\_Muhammed](https://forum.biobakery.org/u/Amina_Muhammed)\ **Replies:** 1\ **Last updated:** [September 10, 2021, 3:42pm UTC](https://forum.biobakery.org/t/graphlan-tree-file/2558 "2021-09-10T15:42:38Z")
I have installed graphlan and run the command lines as illustrated in this link I got the files from here: Tree file: guide.txt Annotation file: guide\_rings.txt I have downloaded those files on my PC and I have run… [Next page](https://forum.biobakery.org/c/infrastructure-and-utilities/graphlan/17.md?page=1)