How to download an alignment from TreeBase according to accession numbers

Question

[Yongjie Zhang]

Hi,

Could anybody tell me how to download an alignment from TreeBase if I have the accession number provided by the author of a paper?

Thanks in advance.
Yongjie

Answer 1

[Joseph Hughes]

Go to TreeBase, click on the "search TreeBase" button on the left, type in the study number from the paper (e.g., S1234), click search.

Tick the box that corresponds to your study and on the right-click the little icon of a document with a green arrow pointing down to download the NEXUS formatted file. This file has the aligned matrix and the trees in nexus format.

For example, you are interested in study S12813 and here is the screenshot of the result for that accession:

[Yongjie Zhang]

Thanks, Joseph. But do you know why the Treebase accession numbers I want to search, S12813 and 12641, have no matching studies found?

[Joseph Hughes]

Accession 12641 does not exist but I found something for S12813. Contact the authors to check whether they have made a typo with the accession number, or alternatively search TreeBase by author name or species name.