Bioinformatics
and Pharmacogenomics Laboratory
Crann: A program for detecting adaptive evolution in protein-coding DNA sequences.
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.
Authors:
Chris Creevey (Email: chris.creevey@may.ie)
James McInerney (Email: james.o.mcinerney@may.ie)
Copyright © Chris Creevey 2002
Downloads (Binary executables): Crann 1.04 is the current version, updated 15th April 2003
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The source code is available on request from Chris Creevey.
Information on downlading, installing and running Crann is available in the Crann User 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)
Help:
Li, W.-H., C.-I. Wu, et al. (1985). A new method for estimating synonymous and nonsynonymous rates of nucleotide substitution and considering the relative likelihood of nucleotide and codon changes. Mol. Biol. Evol. 2: 150-174.
Li, W. H. (1993). Unbiased Estimation of the Rates of Synonymous and Nonsynonymous Substitution. Journal of Molecular Evolution 36: 96-99.
Messier, W. and C. B. Stewart (1997). Episodic adaptive evolution of primate lysozymes. Nature 385: 151-4.
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