News:CAFE v4.0 available
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5.9 years ago
Ben Fulton ▴ 140

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 hahnlabcafe@googlegroups.com.

CAFE phylogenetics News • 2.9k views
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Hello!I am a graduate student from China.There are some questions I want to ask you.

  1. 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.

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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?

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@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.

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