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Prof. Itay Mayrose Lab - Plant Evolution, bioinformatics, & comparative genomics

We are working on improving OneTwoTree for enhanced flexibility and a better user interface.
If you run into problems please email and specify the job ID.
Thank you!

How to use OneTwoTree® pipeline?
When using OneTwoTree please cite us: Drori M, Rice A, Einhorn M, Chay O, Glick L, Mayrose I. OneTwoTree: An online tool for phylogeny reconstruction. Mol Ecol Resour. 2018;00:1-8.

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Running options:
Phylogeny reconstruction
Obtain orthologous loci


Upload a file with your list of TaxIDs/taxa names (see explenation on NCBI), or paste the list in the window (available only for:
mammals, invertebrates, plants, primates, rodents and vertebrates. last updated Dec 2017).
Taxa names should be separated by a newline. Genera and species should be separated by a space or an underscore:

Filtering options

Filter intraspecific varieties Merge intraspecific varieties
Filter hybrids
Filter open nomenclature

Name resolution

Name resolution options:

Naming-database selection:

Naming-database selection:


Rerun your data:

Advanced parameters

Outgroup selection:

User defined Automatic selection

Choose genome:


Clustering options:
Clustering software:
OrthoMCL pairwise similarity cutoff:
OrthoMCL inflation parameter:
BLASTCLUST percent identity:
BLASTCLUST coverage length:

Alignment options:
MSA software:
Max iterations:
Pairwise alignment method:

MSA filter:

Phylogeny inference:
Nucleotide model:
Enable bootstrap:
Nucleotide model:
Enable bootstrap:

On Off
Tree type:

Constraint tree:

Divergence time estimation:


Node dating: