CAFE v4.0 is now available on Github. This release includes an improved HTML report formatting option and fixes for various minor bugs. Please visit the CAFE website (https://hahnlab.github.io/CAFE/ ) where you will find the user manual and a tutorial on the usage of CAFE.
The purpose of CAFE is to analyze changes in gene family size in a way that accounts for phylogenetic history and provides a statistical foundation for evolutionary inferences. The program uses a birth and death process to model gene gain and loss across a user-specified phylogenetic tree. The distribution of family sizes generated under this model can provide a basis for assessing the significance of the observed family size differences among taxa.
Post questions here or to the mailing list at firstname.lastname@example.org.
Hello!I am a graduate student from China.There are some questions I want to ask you.
Some errors occurred when I ran：
python python_scripts/ cafetutorial_longest_iso.py-d twelve_spp_proteins/
Report errors: File "python_scripts/cafetutorial_longest_iso.py", line 71 print fa_file_name + "...done!"
SyntaxError: Missing parentheses in call to 'print'. Did you mean print(fa_file_name + "...done!")?
2.When I download cafe_tutorial files through web download link, remind me that it is not Shared files:
The link you're trying to access can't be used to share files. Please ask The file owner to provide you with a Shared link instead.
Is there Shared link available for the user to download?
Thank you very much for your help.
The first one sounds like a version conflict. CAFE expects python 2.6 or newer. Do you happen to have python3 installed as the default?
@BenFulton Hello sir, what basic RAM memory needed for CAFE. I have to work on Fungal genome having sequences (appox. 20K) Kindly suggest basic RAM for system Thank you very much for your help.