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RaxML fails -- Empirical base frequency for state number 2 is equal to zero in DNA data partition No Name Provided

I have the same error. Did you find a solution?

RaxML fails -- Empirical base frequency for state number 2 is equal to zero in DNA data partition No Name Provided

Thank you. I will try

ValueError: invalid literal for int() with base 10: '5_42'

I meet the same error. Do you have solution?

ValueError: invalid literal for int() with base 10: '5_42'

I have solved my problem. Because my tree file has extra "." . I checked your input file. Maybe you can replace the species name with no dots, and remove...

ValueError: invalid literal for int() with base 10: '5_42'

tree (((((acch:74.8509,(((rhde:7.0997,rhwi:7.0997):3.6345,rhsi:10.7342):00.8280,rhov:11.5623):63.2887):8.2057,casi:83.0566):0.056636,dilo:88.7201):18.2580,prvu:106.9782):4.1897,soly:111.1678) This is an example. 我再用中文解释一下，去掉所有空格和bootstrap的信息，仅保留时间信息。看上面@gwct的评论也是这个意思，计算扩张收缩的基因家族数量没有问题，但是如果要用report这个汇总的脚本就需要对把树上多余的标签信息去掉，