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anastasiiakim / PRANC

PRANC is used to compute probabilities of ranked phylogenetic gene trees given a species tree under coalescent process.
MIT License
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ERROR: not all ranks! on -rank_trees #2

Closed MaoYafei closed 4 years ago

MaoYafei commented 4 years ago

Hi All,

I am trying to run pranc but I found that I have some issues on running. Could you help me to figure them out?

test examples:

$ cat unrgt_5taxon.txt ((B,E),(A,(C,D))); $ pranc -rank_trees unrgt_5taxon.txt $ cat outRankTopos.txt ((B:3,E:3):1,(A:2,(C:1,D:1):1):2); ((B:2,E:2):2,(A:3,(C:1,D:1):2):1); ((B:1,E:1):3,(A:3,(C:2,D:2):1):1);

my data

cat treedist_1.txt (Orangutan,(HMO,(NLE,(SSY,HLE)))); $ pranc -rank_trees treedist_1.txt ERROR: not all ranks!

Is there something wrong with my tree?

Thank you so much.

Best, Yafei

anastasiiakim commented 4 years ago

PRANC didn't know how to work with the long taxa names for -rank_trees. The issue is now fixed. The output looks like this: (Orangutan:4,(HMO:3,(NLE:2,(SSY:1,HLE:1):1):1):1);