# Can't change annotation colors on graphlan cladogram

**URL:** https://forum.biobakery.org/t/cant-change-annotation-colors-on-graphlan-cladogram/7185
**Category:** GraPhlAn
**Created:** [June 21, 2024, 10:09pm UTC](https://forum.biobakery.org/t/cant-change-annotation-colors-on-graphlan-cladogram/7185 "2024-06-21T22:09:59Z")
**Posts on this page:** 1
**Page:** 1

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### Author: ![rachel](https://avatars.discourse-cdn.com/v4/letter/r/46a35a/32.png) [@rachel](https://forum.biobakery.org/u/rachel)
#### Post date: [June 21, 2024, 10:09pm UTC](https://forum.biobakery.org/t/cant-change-annotation-colors-on-graphlan-cladogram/7185/1 "2024-06-21T22:09:59Z")

</div>

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 export2graphlan v0.22 and graphlan v1.1.3 on a system running Rocky Linux 8.9. I’m not having any issue generating a cladogram, but I can’t change the background (shaded area) colors using the background\_annotation\_parameter either with export2graphlan or graphlan. Colors always default to green and blue for the background shading. I see there is a way to manually adjust colors in the annotation file, however this will be a tedious process so I was wondering if there’s a quicker way around it. Or, is there a way to turn off the annotation shading altogether? I may be misunderstanding which parameter controls the shaded areas and/or how to modify it.

```auto
# I want shaded areas of red and green instead of green and blue
export2graphlan.py -o vancPostNeoPost_lefseInput.res -t tree_1.txt -a annotations_1.txt --annotations 2 --external_annotations 3,4,5 --background_colors "#cc0000, #38761d"

graphlan_annotate.py --annot annotations_1.txt tree_1.txt tree_2.txt

graphlan.py tree_2.txt tree_2.pdf --format pdf

```

 ![snip](https://canada1.discourse-cdn.com/flex027/uploads/biobakery/original/2X/3/3581ed697be57ab71f0d9b96b69d48ef2d212a3b.jpeg)

Any help is appreciated.

Thanks, R