Problem with a tree for ClonalFrameML
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3.3 years ago
little_more ▴ 70

I'm trying to run ClonalFrameML using a tree:

((((./genomes/GCA_000008865.2_ASM886v2_chromosome.fna:0.00146992883339864015,./genomes/GCA_000245515.1_ASM24551v1_chromosome.fna:0.00089815475169334675):0.02252687048062455497,((((./genomes/GCA_000497505.1_ASM49750v1_chromosome.fna:0.00067857569383474254,./genomes/GCA_000012005.1_ASM1200v1_chromosome.fna:0.00633802124574869667):0.03099057816646913141,./genomes/GCA_002854065.1_ASM285406v1_chromosome.fna:0.02399793470217133351):0.00378174809707187108,((./genomes/GCA_002196495.1_ASM219649v1_chromosome.fna:0.00000100000050002909,./genomes/GCA_002196475.1_ASM219647v1_chromosome.fna:0.00019992285965354421):0.00957796193772160465,./genomes/GCA_002058765.1_ASM205876v1_chromosome.fna:0.01289160946157907883):0.01344824749473950282):0.00514459801470873966,./genomes/GCA_000520035.1_ASM52003v1_chromosome.fna:0.02281556087364138008):0.00389031049851667251):0.01179754721585075765):0.01950019871133733262,./genomes/GCA_001677475.1_ASM167747v1_chromosome.fna:0.05615742142924622093);


But I get an error:

WARNING: Token: ((./genomes/GCA_000008865.2_ASM886v2_chromosome.fna:0.00146992883339864015,./genomes/GCA_000245515.1_ASM24551v1_chromosome.fna:0.00089815475169334675):0.02252687048062455497,((((./genomes/GCA_000497505.1_ASM49750v1_chromosome.fna:0.00067857569383474254,./genomes/GCA_000012005.1_ASM1200v1_chromosome.fna:0.00633802124574869667):0.03099057816646913141,./genomes/GCA_002854065.1_ASM285406v1_chromosome.fna:0.02399793470217133351):0.00378174809707187108,((./genomes/GCA_002196495.1_ASM219649v1_chromosome.fna:0.00000100000050002909,./genomes/GCA_002196475.1_ASM219647v1_chromosome.fna:0.00019992285965354421):0.00957796193772160465,./genomes/GCA_002058765.1_ASM205876v1_chromosome.fna:0.01289160946157907883):0.01344824749473950282):0.00514459801470873966,./genomes/GCA_000520035.1_ASM52003v1_chromosome.fna:0.02281556087364138008):0.00389031049851667251):0.01179754721585075765
Single descendant found
ERROR: convert_NewickTree_to_marginal_tree(): Number of nodes (20) and number of tips (10) incompatible with a strictly bifurcating rooted tree


What's the problem here?

trees ClonalFrameML • 712 views
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Something about the internal node structure of your tree must be wrong, somehow. For a perfectly bifurcating tree, there should be 2n - 3 nodes in the tree. You somehow have 20 it seems, but with 10 tips, you should only have 17.

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Yeah, I understand that. But I don't see any problem in the tree. It seems bifurcating enough to me. :-)

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How did you generate the tree?