# GraPhlAn **URL:** https://forum.biobakery.org/c/infrastructure-and-utilities/graphlan/17.md?page=1 [Latest](https://forum.biobakery.org/latest.md) · [Categories](https://forum.biobakery.org/categories.md) **Page:** 2 --- ## [Invalid syntax message when running export2graphlan](https://forum.biobakery.org/t/invalid-syntax-message-when-running-export2graphlan/992)
**Author:** [@elenu](https://forum.biobakery.org/u/elenu)\ **Replies:** 4\ **Last updated:** [August 9, 2021, 11:52pm UTC](https://forum.biobakery.org/t/invalid-syntax-message-when-running-export2graphlan/992 "2021-08-09T23:52:05Z")
Hello, I am running GraPhlAn taking as a reference the turorial: I tried to run the step 1 (to create the GraPhlAn input files), but I got an error message: File "/home/eyre/anaconda3/bin/export2graphlan.py", line… --- ## [Graphlan - Names overlapped](https://forum.biobakery.org/t/graphlan-names-overlapped/2380)
**Author:** [@Valter](https://forum.biobakery.org/u/Valter)\ **Replies:** 2\ **Last updated:** [July 17, 2021, 12:46am UTC](https://forum.biobakery.org/t/graphlan-names-overlapped/2380 "2021-07-17T00:46:29Z")
Graphlan - Names overlapped Hi everyone, I have been trying to separate the names on the figure to better visualization, but I couldn’t find a proper command to do it. Used commands: tail -n +2 merged\_abundance\_table… --- ## [How can I annotate the internal nodes from Newick tree?](https://forum.biobakery.org/t/how-can-i-annotate-the-internal-nodes-from-newick-tree/2342)
**Author:** [@kazuma](https://forum.biobakery.org/u/kazuma)\ **Replies:** 1\ **Last updated:** [July 16, 2021, 3:26pm UTC](https://forum.biobakery.org/t/how-can-i-annotate-the-internal-nodes-from-newick-tree/2342 "2021-07-16T15:26:27Z")
Dear all, I would like to create an annotated tree from the output (.nwk) of PhyloPhlAn 3 using GraPhlan. I tried to annotate the internal nodes, but I can’t get it to work. graphlan\_annotate.py tree.newick annot.xml… --- ## [No plotting phylum level in Graphlan](https://forum.biobakery.org/t/no-plotting-phylum-level-in-graphlan/2297)
**Author:** [@Francisco\_Daniel\_Dav](https://forum.biobakery.org/u/Francisco_Daniel_Dav)\ **Replies:** 3\ **Last updated:** [July 12, 2021, 12:15pm UTC](https://forum.biobakery.org/t/no-plotting-phylum-level-in-graphlan/2297 "2021-07-12T12:15:43Z")
Dear all, I would like to kindly ask you for your help. I am currently using Graphlan and I want to plot the phylum, family and genera to the tree (–annotations 2,5,6) but only shows the family and genera level. I used… --- ## [Adding a scale bar to a circle plot/ how do I know the scale of my tree](https://forum.biobakery.org/t/adding-a-scale-bar-to-a-circle-plot-how-do-i-know-the-scale-of-my-tree/2003)
**Author:** [@brijon](https://forum.biobakery.org/u/brijon)\ **Replies:** 1\ **Last updated:** [June 3, 2021, 6:06pm UTC](https://forum.biobakery.org/t/adding-a-scale-bar-to-a-circle-plot-how-do-i-know-the-scale-of-my-tree/2003 "2021-06-03T18:06:57Z")
Hi, Ive been asked to add a scale bar to a circle plot I made in graphlan, to my knowledge its not possible to add a scale bar or labelled branch lengths to a circleplot within graphlan? If so is there a way I can wor… --- ## [Graphlan metadata name manipulation](https://forum.biobakery.org/t/graphlan-metadata-name-manipulation/2132)
**Author:** [@Jeffrey\_Chiu](https://forum.biobakery.org/u/Jeffrey_Chiu)\ **Replies:** 1\ **Last updated:** [June 2, 2021, 10:27pm UTC](https://forum.biobakery.org/t/graphlan-metadata-name-manipulation/2132 "2021-06-02T22:27:17Z")
So I have a tree generated for strainphlain with metadata added, but the png I generate with graphlan cuts off the value of the SubjectID I want. For example: My subject ID would be Rhyticeros\_undulatus in my tre.metad… --- ## [How to stop let Branch Color changes with clade\_marker\_color?](https://forum.biobakery.org/t/how-to-stop-let-branch-color-changes-with-clade-marker-color/1156)
**Author:** [@Ivy-ops](https://forum.biobakery.org/u/Ivy-ops)\ **Replies:** 1\ **Last updated:** [January 15, 2021, 3:42am UTC](https://forum.biobakery.org/t/how-to-stop-let-branch-color-changes-with-clade-marker-color/1156 "2021-01-15T03:42:00Z")
Please direct your questions/bugs to bioBakery Support Forum under specific categories… Hi Developer, I use the global setting for the clade marker, results to the current status: the branch color changes with the clad… --- ## [Graphlan error (Classes not implemented for external annotations)](https://forum.biobakery.org/t/graphlan-error-classes-not-implemented-for-external-annotations/965)
**Author:** [@mjamy](https://forum.biobakery.org/u/mjamy)\ **Replies:** 1\ **Last updated:** [January 13, 2021, 2:33pm UTC](https://forum.biobakery.org/t/graphlan-error-classes-not-implemented-for-external-annotations/965 "2021-01-13T14:33:52Z")
Hi all! I am trying to generate a tree figure using Graphlan. But I am getting an error when using the graphlan\_annotate.py script: Classes not implemented for external annotations. Here is the command used: graphl… --- ## [Export2graphlan: Traceback](https://forum.biobakery.org/t/export2graphlan-traceback/586)
**Author:** [@Philipp\_Licht](https://forum.biobakery.org/u/Philipp_Licht)\ **Replies:** 3\ **Last updated:** [June 22, 2020, 3:19pm UTC](https://forum.biobakery.org/t/export2graphlan-traceback/586 "2020-06-22T15:19:16Z")
Hello, I am currently running throuh the Metaphlan3 wiki tutorial (https://github.com/biobakery/biobakery/wiki/metaphlan3) with the example data as well as own data. When it comes to creating Graphlan input files with e… [Previous page](https://forum.biobakery.org/c/infrastructure-and-utilities/graphlan/17.md)