Significant contractions are marked in magenta, significant expansions are marked in green (p<=0.001 = ***, p<=0.01 = **, p<=0.05 = *). These trees will only be created for families that showed a significant (p<=0.05) expansion/contraction at the node "Isoptera", which is the last common ancestor of "zne" and "mna". Further family-wise trees will be created and dumped in the directory "test/families". The summary tree ("summary.pdf") will show the whole phylogeny and the number of expansions and contractions (including insignificant ones!) as shown below.
#Fig tree cafe pdf#
This reads "example_result.cafe" and dumps all figures in PDF format to the directory "test/". CAFE_fig.py example_result.cafe -c Isoptera=zne,mna -pb 0.05 -pf 0.05 -dump test/ -g. To recreate the plots shown above, use this command: Significant expansions are shown in green, significant contractions in magenta. Numbers and node sizes represent the family size at each node. The numbers of expanded/contracted families (+/-), and the estimated gene gain/lossĮxample output for a specific gene family. Summary tree that shows the average expansion/contraction (radius of node circles), Output format for the tree figures when using -dumpĬount and write down the number of *all* expansionsĪnd contractions (default: only count significant g GFX_OUTPUT_FORMAT, -gfx_output_format GFX_OUTPUT_FORMAT The specified directory instead (default: off) d DUMP, -dump DUMP don't open trees in a window, write them to files in pf PF family p-value cutoff (default: 0.05) pb PB branch p-value cutoff (default: 0.05) Is the name of the last common ancestor of the two Only show families that are expanded/contracted at h, -help show this help message and exit Report_cafe the file report.cafe (or similar name) Parses a CAFE output file (.cafe) and plots a summary tree that shows theĪverage expansion/contraction across the phylogeny a tree that shows whichĬlades evolved under the same lambda (if available) and a gene familyĮvolution tree for each user-specified gene family. This ETE3 version runs well with PyQt4 but not PyQt5, so if you're experiencing issues it's worth a try to switch to PyQt4. It's important that you use ETE3 version 3.0.0b35 since it appears that the latest ETE3 version causes problems that are beyond my control (see issue #1). families that the user specified by ID or families that showed significant change at a user-specified clade of interest
Here, I provide such a custom script.ĬAFE_fig takes a. The visualization and interpretation of CAFE results usually requires custom
Inferences about changes in gene family size.
#Fig tree cafe software#
CAFE (Computational Analysis of gene FamilyĮvolution) is a software that provides a statistical foundation for evolutionary
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