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caseywdunn / agalmar

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Parse nhx trees #1

Open caseywdunn opened 8 years ago

caseywdunn commented 8 years ago

At present gene trees are only parsed in newick format. Parse in nhx format to preserve information on duplications etc.

A few packages do this, including ggtree: https://bioconductor.org/packages/release/bioc/vignettes/ggtree/inst/doc/treeImport.html#parsing-nhx-tree

caseywdunn commented 8 years ago

ggtree can now read a nhx tree from a string, https://github.com/GuangchuangYu/ggtree/pull/55 .

syntax is:

nhx = read.nhx( textConnection( nhx_text )