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Effective Phylogenetic Compression with TreeZip

Suzanne Matthews, SeungJin Sul, Tiffani Williams
2010 Nature Precedings  
To combat the cost of storage and to facilitate the transfer of these large tree files, we developed a new compression algorithm called TreeZip that reduces the requirements for storing large collections  ...  of evolutionary trees over standard compression methods.  ...  Our results strongly suggest that TreeZip is a powerful and effective approach for compressing large collections of phylogenetic trees. Conclusion.  ... 
doi:10.1038/npre.2010.4613.1 fatcat:fpy5terjkfg35lspaqaxvnd65y

A Novel Approach for Compressing Phylogenetic Trees [chapter]

Suzanne J. Matthews, Seung-Jin Sul, Tiffani L. Williams
2010 Lecture Notes in Computer Science  
We introduce TreeZip, a novel algorithm to compress phylogenetic trees based on their shared evolutionary relationships.  ...  Our results show that TreeZip is very effective, typically compressing a tree file to less than 2% of its original size.  ...  Acknowledgments Funding for this project was supported by NSF under grants DEB-0629849 and IIS-0713618.  ... 
doi:10.1007/978-3-642-13078-6_13 fatcat:htltzu5bazeh5mstitdpdgz3vq

An efficient and extensible approach for compressing phylogenetic trees

Suzanne J Matthews, Tiffani L Williams
2011 BMC Bioinformatics  
Biologists require new algorithms to efficiently compress and store their large collections of phylogenetic trees. TreeZip is a novel method for compressing phylogenetic trees.  ...  TreeZip is an efficient approach for compressing large collections of phylogenetic trees.  ...  KUS-C1-016-04, made by King Abdullah University of Science and Technology (KAUST).  ... 
doi:10.1186/1471-2105-12-s10-s16 pmid:22165819 pmcid:PMC3236838 fatcat:jbr42brib5btzhq25obxqromci

EvoZip: Efficient Compression of Large Collections of Evolutionary Trees [article]

Balanand Jha, David Fernández-Baca, Akshay Deepak, Kumar Abhishek
2019 arXiv   pre-print
Here, we present EvoZip, a new approach for phylogenetic tree compression.  ...  Storing and sharing such large collection of trees requires considerable amount of space and bandwidth.  ...  THE TREEZIP ALGORITHM TreeZip [19] , [20] , [21] , is the current state-of-the-art algorithm for phylogenetic compression, works by exploiting redundancy among the bipartitions in large collections  ... 
arXiv:1910.07819v1 fatcat:xzemsd34gfhhph3amo57m7xvfe

Efficient Coalescent Simulation and Genealogical Analysis for Large Sample Sizes

Jerome Kelleher, Alison M Etheridge, Gilean McVean, Yun S. Song
2016 PLoS Computational Biology  
Analysing the results of simulations also presents a substantial challenge, as current methods to store genealogies consume a great deal of space, are slow to parse and do not take advantage of shared  ...  structure in correlated trees.  ...  Acknowledgments We would like to thank Richard Durbin for helpful discussions and insights. Author Contributions Conceived and designed the experiments: JK AME GM. Performed the experiments: JK.  ... 
doi:10.1371/journal.pcbi.1004842 pmid:27145223 pmcid:PMC4856371 fatcat:ianupvcd5rdl5gnkdb2wqz2o3q