Common LISP: the language (2nd ed.)
Common LISP: the language (2nd ed.)
Computer-Aided Reasoning: An Approach
Computer-Aided Reasoning: An Approach
Requirements of Phylogenetic Databases
BIBE '03 Proceedings of the 3rd IEEE Symposium on BioInformatics and BioEngineering
Design of a Lisp machine - FLATS
LFP '82 Proceedings of the 1982 ACM symposium on LISP and functional programming
Function memoization and unique object representation for ACL2 functions
ACL2 '06 Proceedings of the sixth international workshop on the ACL2 theorem prover and its applications
ACL2 '06 Proceedings of the sixth international workshop on the ACL2 theorem prover and its applications
An Experimental Analysis of Consensus Tree Algorithms for Large-Scale Tree Collections
ISBRA '09 Proceedings of the 5th International Symposium on Bioinformatics Research and Applications
A novel approach for compressing phylogenetic trees
ISBRA'10 Proceedings of the 6th international conference on Bioinformatics Research and Applications
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Phylogenetic tree searching algorithms often produce thousands of trees which biologists save in Newick format in order to perform further analysis. Unfortunately, Newick is neither space efficient, nor conducive to post-tree analysis such as consensus. We propose a new format for storing phylogenetic trees that significantly reduces storage requirements while continuing to allow the trees to be used as input to post-tree analysis. We implemented mechanisms to read and write such data from and to files, and also implemented a consensus algorithm that is faster by an order of magnitude than standard phylogenetic analysis tools. We demonstrate our results on a collection of data files produced from both maximum parsimony tree searches and Bayesian methods.