How do I convert nexus files to newick format?

Tanweer Alam Popular answer

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'.

Tanweer Alam

Anna Liza Kretzschmar

Hi Tanweer,

thanks for your answear. This step precedes the tree generation though - the alignment needs to be in newick format. For converting the alignment I've tried using readseq.jar for converting .xml to .nexus, however neither of them could be read by Geneious. In Beauti, the GUI for beast, I couldn't see an option I export in a different file format and most of the conversion scripts I saw online deal with trees not alignment.

One possibility seems DendroPy but my Python skips are still pretty limited.

Csaba Csuzdi

Dear Anna,

Might be I'm wrong but I think Newick format is just for trees. I never heard about newick formatted alignment

Meriadeg Ar Gouilh

Dear Anna, dear all, Csaba is right, nexus file use newick format (parenthetic) for tree representation. From what I understand, the quickest way to solve your problem and go from .xml alignement to nexus format will be using a simple text editor (preferably copy paste the alignement in a TextEdit file on mac os x) and copy / search / replace elements. For exemple, replace regular expressions

Zhe Zhao

figtree

Tyler Chafin

As Artur and Csaba said, the Newick format input for ASTRAL is for gene trees, since the purpose of ASTRAL is to estimate a species tree with maximized quartet concordance with a given set of input gene trees... Thus you will need to first estimate gene trees from your data.

This presents several things to think about:

How to make some gene trees? This is handled easily enough. We usually use RAxML to generate our gene tree input for ASTRAL, although ASTRAL is not among my favorite "species tree" inference implementations so I don't often use it.

Can you/ should you make gene trees? What kind of data do you have? How was it generated? If your independent "loci" are very short, than they likely do not contain enough phylogenetic information to infer a resolved "gene tree". If this is the case, you might think about forgoing programs which require gene trees as input, and use instead species-tree estimators which simultaneously integrate over gene trees, like the SNAPP module for BEAST (although if lacking sufficient computational resources, this might not be possible in a reasonable time). I also like SVDQuartets, which is very quick. For screening purposes, this might be a better bet as I've found it to be substantially faster than inferring many thousands of gene trees, parsing the results, and then feeding these into ASTRAL.

Can you resolve a species tree? Is the species tree method being employed appropriate for the data you have? Any phylogenetic package can regurgitate an answer if you feed it the proper information. Does the method you are using take gene tree uncertainty into account? What are the potential sources of gene tree discordance (e.g. hybridization vs. deep coalescence), and does the species tree method you are using consider this? Do your data otherwise violate any underlying assumptions of the program? It is necessary to (at least at the conceptual level, if not at the algorithmic level) understand the inner workings of the program, and to adjudicate on the validity the results. Simply resolving a species tree means pretty much "squat" if methods are misapplied or results are misinterpreted. Attached a recent paper that I like that talks about this problem and some implications.

Anna Liza Kretzschmar

Dear all,

My apologies about this thread - I had responded to each of the answers back in January on my phone and they obviously didn't upload (it died shortly after, a bunch of weird stuff like tis happened).

Casab and the following responses were right, newick is for trees only. I had my wires crossed with reading the documentation for beast and ASTRAL at the same time. So thank you for your responses and helping me to work out that error!

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