1
$\begingroup$

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

$\endgroup$
2
$\begingroup$

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.

$\endgroup$
  • $\begingroup$ I don't see how to export, would help if you wouldn't mind explaining. $\endgroup$ – Lance Pollard Sep 18 '18 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 '18 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 '18 at 10:17
1
$\begingroup$

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.

$\endgroup$

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.