Some species have 0 contracted and expanded gene families

[yuanw-18]

Hi!

When I used this software, four out of the fifteen species showed zero expanded and contracted gene families. I don't know why this issue occurred. Could you please advise me on how to improve it? I’m not sure if this is related to me splitting some allotetraploids into diploids （Aa & Ba）.

These are some results and code.

$cafe5 -i gene_families_filter.txt -t ConvertedTree.tre -c 40 -k 2 -p -o output

$cat Gamma_results.txt
Model Gamma Final Likelihood (-lnL): 181245
Lambda: 0.0055548523385088
Maximum possible lambda for this topology: 0.0210061
215 values were attempted (0% rejected)
Alpha: 0.553327

Thanks~

Yuan

[benfulton]

It seems like something in the visualization of the output has gone wrong. I can’t imagine why CAFE wouldn’t literally give an answer. Are there numbers in the output files produced by the application?

[hduidui]

You can check the tree file, and there should be no blank !!!