CAFE5 output visualization

[Fantacooke2]

Dear all ,

I hope you are doing well.

I am working with CAFE5 and analyzing the results from the following command:

cafe5 -i ./filtered.cafe.input.txt -t ./tree.nwk -p -y ./lambda_tree.nwk -o multiplelambda

This produced several output files, including Base_asr.tre, Base_change.tab, and Base_results.txt, among others. I would like to visualize gene family expansion and contraction on each evolutionary branch, with numbers indicating the expansions, contractions, and significantly (p-value ≤ 0.01) evolving gene families.

I tried CAFEPLOTTER but as mentionned previously by @YuzhouGong, there is a limitation.
Could you please provide guidance on the best approach to generate a plot showing gene families (Expansions/Contractions/Rapidly evolving families), iedally in three different colors? Specifically, which files should be used, and are there any recommended tools or scripts for this purpose?

I have also tried cafetutorial_report_analysis.py and created the following files:
summary_run_pub.txt
summary_run_node.txt
summary_run_fams.txt
summary_run_anc.txt

But drawing the tree with expansion/contraction/rapidly evolving families using cafetutorial_draw_tree.py is another issue. In CAFE tutorial, this approach was suggested, but, what is the difference between -t and -d options? how do you convert the tree in t to the tree in d?
python python_scripts/cafetutorial_draw_tree.py -i reports/ summary_run1_node.txt -t ’((((cat:68.7105,horse :68.7105) :4.56678, cow:73.2773) :20.7227 ,((((( chimp:4.44417,human :4.44417) :6.68268, orang :11.1268) :2.28586 , gibbon :13.4127) :7.21153 ,( macaque :4.56724 , baboon:4.56724) :16.057):16.0607,marmoset :36.6849) :57.3151):38.738,( rat :36.3024 , mouse :36.3024) :96.4356) ’ -d ’((((cat <0>,horse <2>) <1>, cow <4>) <3>,(((((chimp <6>,human <8>) <7>,orang <10>) <9>,gibbon <12>)

Thank you in advance for your help.

Best regards

[benfulton]

I'm not sure where you're finding cafetutorial_draw_tree.py ? There is a script called cafe5_draw_tree.py in the tutorial directory in v5.1, try using that instead.