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graphlan
GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees. GraPhlAn focuses on concise, integrative, informative, and publication-ready representations of phylogenetically- and taxonomically-driven investigation.
GraPhlAn is available as a Galaxy module, a Conda package, a Docker image, and included in bioBakery (VM and cloud).
We provide support for GraPhlAn users. Please join our Google group designated specifically for GraPhlAn users. Feel free to post any questions on the google group by posting directly or emailing graphlan-users@googlegroups.com.
Table of contents
The following figure shows the workflow of GraPhlAn.
For information about the input formats, and further options, please refer to the GraPhlAn documentation.
GraPhlAn requires an input tree and an annotation file. Download the following demo files for this tutorial:
- Tree file: guide.txt
- Annotation file: guide_rings.txt
Follow these steps to use GraPhlAn Galaxy to visualize results.
Step 1: Go to the Huttenhower Galaxy server: http://huttenhower.sph.harvard.edu/galaxy
Step 2: Upload the tree file
- From the menu on the left-hand side, click on
Get Data
and thenUpload File
- Select the tree file
guide.txt
you just downloaded to your computer - Select the File Format as circl
- Click on the
Execute
button to upload the tree
Step 3: Annotate the tree
- From the menu on the left-hand side, click on
GraPhlAn
and thenAnnotate tree
- For
Input file
, select the tree you just uploadedguide.txt
- From the
Select Clade(s)
list, select the clades you want to be displayed on the figure - In the text field
Annotation Label
, enter*
- From the
Annotation Label Clade Selector
drop-down menu, select theClade and its leaf nodes
option - Click on the
Execute
button
Step 4: Upload the annotation file
- From the menu on the left-hand side, click on
Get Data
and thenUpload File
- Select the annotation file
guide_rings.txt
you just downloaded to your computer - Click on the
Execute
button to upload the annotation file
Step 5: Add rings to the tree
- From the menu on the left-hand side, click on
GraPhlAn
and thenAdd rings to the tree
- Select the annotated tree (produced in the prior step) from the
Input Tree
drop-down menu - Select the annotation file you just uploaded from the
Ring Input File
drop-down menu - Click on the
Execute
button
Step 6: Plot the tree
- From the menu on the left-hand side, click on
GraPhlAn
and thenPlot tree
- Select the tree with rings (produced in the prior step)
- Click on the
Execute
button
The resulting image is shown below:
To look into more visualization options in GraPhlAn, please refer to the GraPhlAn documentation.
GraPhlAn can be installed with Conda or run from a Docker image. Please note, if you are using bioBakery (Vagrant VM or cloud) you do not need to install GraPhlAn because the tool and its dependencies are already installed.
Install with Conda: $ conda install -c biobakery graphlan
Install with Docker: $ docker run -it biobakery/graphlan bash
If you would like to install from source, refer to the GraPhlAn user manual for the dependencies and installation instructions.
For the purpose of this tutorial, we will use the following inputs:
-
Run the following command to annotate the Input tree, hmptree.xml, using the annotation file annot.txt. This will generate an annotated tree (hmptree.annot.xml) :
$ graphlan_annotate.py input/hmptree.xml hmptree.annot.xml --annot input/annot.txt
-
Run the following command to plot the annotated tree in the form of a cladogram. :
$ graphlan.py hmptree.annot.xml hmptree.png --dpi 150 --size 14
The generated cladogram is shown below:
For further information about manipulating the output, other input formats, and more options, please refer to the following wiki pages for more information.
- Step 3 from the MetaPhlAn Pipelines Tutorial
- GraPhlAn documentation.
- HUMAnN 2.0
- HUMAnN 3.0
- MetaPhlAn 2.0
- MetaPhlAn 3.0
- MetaPhlAn 4.0
- MetaPhlAn 4.1
- PhyloPhlAn 3
- PICRUSt 2.0
- ShortBRED
- PPANINI
- StrainPhlAn 3.0
- StrainPhlAn 4.0
- MelonnPan
- WAAFLE
- MetaWIBELE
- MACARRoN
- FUGAsseM
- HAllA
- HAllA Legacy
- ARepA
- CCREPE
- LEfSe
- MaAsLin 2.0
- MaAsLin 3.0
- MMUPHin
- microPITA
- SparseDOSSA
- SparseDOSSA2
- BAnOCC
- anpan
- MTXmodel
- MTX model 3
- PARATHAA