Frequently asked questions

Do I need to register to use T-BAS?

Yes. T-BAS leverages computational resources at CIPRES and registration is required to track usage statistics and user quotas. Registration is also required to download reference trees, alignments and metadata.

How many loci can T-BAS handle?

Up to 250 loci can be examined using phylogeny-based methods.

What is the difference between MEP and T‑BAS archives?

MEP run archive

  • Started saving XML archive files May 3 2019, and added .mep file name extension for the archives in December 2019.
  • MEP are for building and adding more sequences with the caveat that if sequences were clustered using placement then all the sequences in an OTU are included in the archive for that placement, but would be lost if the MEP file is used to place a second time.
  • MEP will save all updates to colors and metadata.
  • Previously placed unknown sequences are considered as taxa in the new reference MEP tree.
  • MEP files are useful for building larger reference trees from previous placements.
  • MEP archives can be easily retrieved by the user using the MEP archive tool (

T-BAS run archive

  • Keeps a copy of all the relevant files created from a placement run.
  • Will not include any changes made to the metadata and colors.
  • All the unknown sequences within each OTU can only be downloaded.
  • Unknowns are labeled as such in the T-BAS tree.
  • Cannot use this format to build new reference trees using placed unknowns - must save as MEP first.
  • After 30 days the user will not have access to T-BAS archives so must be downloaded soon after run is finished.
  • Can upload into T-BAS using archive tool (

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