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I have a phylogenetic tree in Newick format. A sample from the full string looks like this: "...(tet_rpg.hmm_GCA_000638155.1_seq1:0.001565531,tet_rpg.hmm_GCA_000507745.1_seq1:0.001565235)0.000:5e-09,...". I understand that distances are given by the number after a colon, but what do numbers immediately following closed parentheses signify? In the sample above, what does "0.000" represent?

Gragas
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This is bootstrap values. The confidence level of clade existence.

Classic source

Vovin
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    Is that necessarily true? Could not the number denote an alternative measure of clade confidence, such as posterior probability – or indeed any arbitrary clade label? – Martin Smith Mar 08 '22 at 08:51
  • @MartinSmith Of course, yes. For instance, if we talk about BEAST and other Bayesian tools. I just gave the answer about common use. – Vovin Mar 08 '22 at 20:28