Question: how to convert a NEXUS treefile to a Newick ultrametric treefile
1
gravatar for chenllianfu
5.0 years ago by
chenllianfu10
China
chenllianfu10 wrote:

I want to konw how to convert a general treefile to a ultrametric treefile. I have maken a species tree using RAxML to analysis several hundreds single copy genes. And now, i need to use CAFE to analysis the protein families expansion. But CAFE need a Newick treefile as input. Could anyone give a suggestion?

phylogenesis • 8.8k views
ADD COMMENTlink modified 5.0 years ago by rwn470 • written 5.0 years ago by chenllianfu10
1
gravatar for rwn
5.0 years ago by
rwn470
United Kingdom
rwn470 wrote:

If you need to convert just one tree from Nexus to Newick, the simplest thing might be just to open it up in a tree-viewing program like FigTree (http://tree.bio.ed.ac.uk/software/figtree/), and export as a Newick: File > Save Trees > Select 'Newick' from menu. 

Newick treefiles are of course not necessarily ultrametric, but you can convert your tree into a cladogram (a tree with all branch lengths = 1, which is what I think you might mean) using the options within FigTree: Trees > Transform Branches > Select 'Cladogram'.

ADD COMMENTlink written 5.0 years ago by rwn470
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