Computer-Aided Reasoning: An Approach
Computer-Aided Reasoning: An Approach
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
A compressed format for collections of phylogenetic trees and improved consensus performance
WABI'05 Proceedings of the 5th International conference on Algorithms in Bioinformatics
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
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Biologists studying the evolutionary relationships between organisms use software packages to solve the computational problems they encounter. Several of these problems involve the production and analysis of phylogenetic trees. We present our system for phylogenetic tree manipulation, TASPI, which was designed to allow the specification and verification of various tree operations, while giving good execution performance. The first aspect of TASPI is a new format for storing and manipulating phylogenetic trees that significantly reduces storage requirements while continuing to allow the trees to be used as input to post-tree analysis. We also prove the correspondence of this format to another tree format. In addition, we give a consensus algorithm with verified guards that is faster by an order of magnitude than standard phylogenetic analysis tools.