Support extended Newick?

[cossio]

It seems the package cannot read extended Newick format trees?

I'm having trouble in particular reading trees stored in RFAM (https://docs.rfam.org/en/latest/api.html?highlight=nhx#tree-data). For example,

http://rfam.org/family/RF00360/tree/

[mkborregaard]

Is there a specification for extended newick? Quick search brings up https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-9-532

[richardreeve]

@cossio - I'm sure it's too late now, but for what it's worth, I'm finally finding some time to rewrite the parser. I'm hoping to write an improved nexus/newick parser that will allow you to import and export trait values using the same format that BEAST uses - https://beast.community/nexus_metacomments.html - but I haven't heard of RFAM and unless there's a clear definition of it somewhere, I'm unlikely to adopt that too as I've never seen it before.

[richardreeve]

The parser reads and writes the metacomment format to set node and branch data, but given there's no obvious specification for this RFAM format, and it actually doesn't look much like the standard newick or nexus tree format, it doesn't seem likely we'll be able to support it, sorry.

[richardreeve]

Interestingly I've just found a definition for extended newick on wikipedia - https://en.wikipedia.org/wiki/Newick_format#Extended_Newick - but it looks nothing like this! I've also found nhx format in the same entry - https://en.wikipedia.org/wiki/Newick_format#New_Hampshire_X_format - but that also looks nothing like this. I think it's a bit of a minefield, and I'm not sure it'll be possible to support any of them.