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LKremer / CAFE_fig

A tool to extract and visualize the results of CAFE (Computational Analysis of gene Family Evolution)
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The same number of significantly expanded and contracted families #5

Open methylome opened 4 years ago

methylome commented 4 years ago

Hello,

I really like this fantastic program to draw Cafe output files. When I used it with my data, the numbers of significantly expanded and contracted families are the same while the example data showed the different numbers. Could you check if this is correct?

Thanks, Justin cafe_result.txt summary.pdf

dingcaojin commented 2 years ago

@methylome Hi，I have the same problem. Can you tell me if you've solved it.

Thanks, Ding

methylome commented 2 years ago

@dingcaojin I haven't solved it.

Thanks, Justin

YuzhouGong commented 7 months ago

Hi guys, I have encountered a similiar problem, when I used the example data without the --count_all_expansions option, the result showed same numbers in expanded and contracted gene families, like this: 图片 But when I added --count_all_expansions, the result seemed to be correct, like this: 图片 As for my own data, because I'm using CAFE5, the result generated by cafe_fig is not correct when skipping --count_all_expansions, all nodes show +0 -0 pattern on the phylogenetic tree. Seems like cafe_fig must rely on option count_all_expansions to draw the right number on trees.