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Wondering if there is a tree of life in Text format for open data sharing.

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Perhaps not though the tree of life website, but the Open Tree of Life exists to fulfil this need. You can export newicks of nodes which you are interested in.

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  • $\begingroup$ I don't see how to export, would help if you wouldn't mind explaining. $\endgroup$
    – Lance
    Sep 18, 2018 at 7:53
  • $\begingroup$ @LancePollard if you look to the bar on the right hand side you should see a heading called "Download subtree as newick string". For large trees this will take you to the repository, but for smaller subtrees there should be an immediate tool. $\endgroup$
    – NatWH
    Sep 18, 2018 at 10:09
  • $\begingroup$ Note that such a huge tree will be difficult for most treeviewers; Dendroscope is probably a good bet $\endgroup$
    – NatWH
    Sep 18, 2018 at 10:17
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The NCBI taxonomy database contains an (as far as I know most complete/up-to-date) database with information about all classified species.

I haven't tested it, but I would guess that its accessible through the E-utilities tools, which will usually allow you to query and download information in xml or raw-text format.

Additionally the whole data the taxonomy database is built on is available on the NCBI ftp-server, they also include readme files so you can figure out how the data is formatted.

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