CRANN: Software for inferring selection


Crann (pronounced ‘crown’) is the Irish word for ‘tree’.

The program Crann has been developed in order to provide fast heuristic methods of detecting adaptive evolution in protein-coding genes. It is important that the user understands the advantages and limitations of these methods. It is also important for the user to know that the software is designed to perform a number of different tasks, however the interpretation of the results is left entirely to the user.

We strongly advise that every user familiarises themseleves with the Crann Manual and the original publications of the methods implemented in Crann.


Chris Creevey (Email:

James McInerney (Email:

The source code is available on request from Chris Creevey.

Information on downloading, installing and running Crann is available in the Crann Manual.

Sample Datasets:

These fasta formatted datasets are those used in the paper by Creevey and McInerney (2002)

Primate Lysozyme (from Messier, W. & Stewart, C-B. (1997) Nature 385, 151-154)

Primate class 1 Major Histocompatibility Complex (MHC) (the human sequences are from Swanson et al. (2001) PNAS 98, 2509-2514)

Mammalian Carbonic anhydrase 1 (from Swanson et al. (2001) PNAS 98, 2509-2514)


Download the program

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Creevey, C. and J. O. McInerney (2003). CRANN: Detecting adaptive evolution in protein-coding DNA sequences Bioinformatics 19: 1726. [link]

Creevey, C. and J. O. McInerney (2002). An algorithm for detecting directional and non-directional positive selection, neutrality and negative selection in protein coding DNA sequences. Gene 300: 43-51. [link]