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Missing the Forest for the Trees: Phylogenetic Compression and Its Implications for Inferring Complex Evolutionary Histories

Cécile Ané, Michael J. Sanderson, Mike Steel
2005 Systematic Biology  
it provides a clear information theoretic rule for determining when a collection of conflicting trees is a better explanation of the data than a single tree.  ...  It selects the hypothesis that simultaneously minimizes the descriptive complexity of the tree(s) plus the data when encoded using those tree(s).  ...  Eulenstein, and Raul Piaggio for discussion of these issues, and Mike Steel, Ming Li, and an anonymous reviewer for helpful comments.  ... 
doi:10.1080/10635150590905984 pmid:15805016 fatcat:lq3znladtva7bozmjngnalcity

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

Balanand Jha, David Fernández-Baca, Akshay Deepak, Kumar Abhishek
2019 arXiv   pre-print
Storing and sharing such large collection of trees requires considerable amount of space and bandwidth.  ...  Phylogenetic trees represent evolutionary relationships among sets of organisms. Popular phylogenetic reconstruction approaches typically yield hundreds to thousands of trees on a common leafset.  ...  We plan to add support for heterogeneous tree collections where each tree can have a different sets of taxa.  ... 
arXiv:1910.07819v1 fatcat:xzemsd34gfhhph3amo57m7xvfe

Phylogenetic Quantification of Intra-tumour Heterogeneity

Roland F. Schwarz, Anne Trinh, Botond Sipos, James D. Brenton, Nick Goldman, Florian Markowetz, Niko Beerenwinkel
2014 PLoS Computational Biology  
Intra-tumour heterogeneity (ITH) is the result of ongoing evolutionary change within each cancer.  ...  Conclusions: Accurate quantification and evolutionary inference are essential to understand the functional consequences of ITH.  ...  The patient also showed strong temporal heterogeneity, as there were large evolutionary distances between samples before and after neoadjuvant chemotherapy (temporal heterogeneity index 3.78, Figure 6B  ... 
doi:10.1371/journal.pcbi.1003535 pmid:24743184 pmcid:PMC3990475 fatcat:rahgrc6fizdtpjjznb22763y4e

RAxML-NG: A fast, scalable, and user-friendly tool for maximum likelihood phylogenetic inference [article]

Alexey Kozlov, Diego Darriba, Tomas Flouri, Benoit Morel, Alexandros Stamatakis
2018 bioRxiv   pre-print
Results: We present RAxML-NG, a from scratch re-implementation of the established greedy tree search algorithm of RAxML/ExaML.  ...  Finally, RAxML-NG introduces several new features, such as the detection of terraces in tree space and a the recently introduced transfer bootstrap support metric.  ...  Acknowledgements We thank Lucas Czech, Pierre Barbera, and members of the RAxML google group for helpful suggestions and testing the beta version of this software.  ... 
doi:10.1101/447110 fatcat:3pjfsixkhzanbmmvqhcb3lnob4

Evolving better wavelet compression schemes

Andreas Klappenecker, Frank U. May, Andrew F. Laine, Michael A. Unser
1995 Wavelet Applications in Signal and Image Processing III  
A prototype implementation of the method is realized as a distributed, parallel implementation on a heterogeneous Unix network.  ...  The results of optimized wavelet based compression schemes are compared with the JPEG compression standard.  ...  Figure 3 : 3 Due to the random operations, evolutionary methods require large populations.  ... 
doi:10.1117/12.217614 fatcat:mbcg2zwmejfqjfoeyeovosxpzi

Evolutionary synthesis of lossless compression algorithms with GP-zip3

Ahmed Kattan, Riccardo Poli
2010 IEEE Congress on Evolutionary Computation  
Both systems outperform a variety of standard compression algorithms and are faster than other evolutionary compression techniques.  ...  More specifically, GP-zip3 evolves and then uses decision trees to predict the performance of GP individuals without requiring them to be used to compress the training data.  ...  RELATED WORK The problem of heterogeneous file compression has been tackled by Hsu in [6] .  ... 
doi:10.1109/cec.2010.5585956 dblp:conf/cec/KattanP10 fatcat:ej7kpvms4bcrnbefsfe3zpzduq

An Evaluation of Phylogenetic Workflows in Viral Molecular Epidemiology [article]

Colin Young, Sarah Meng, Niema Moshiri
2020 bioRxiv   pre-print
However, FastTree 2 was orders of magnitude faster than the other tools, and when the other tools were used to optimize branch lengths along a fixed topology provided by FastTree 2 (i.e., no tree search  ...  Our results indicate that an ideal workflow for viral phylogenetic inference is to (1) use MAFFT to perform MSA, (2) use FastTree 2 under the GTR model with discrete gamma-distributed site-rate heterogeneity  ...  ., the Google Cloud Platform (GCP) Research Credits Program, and the UC San Diego Department of Biomedical Informatics Summer Training Program.  ... 
doi:10.1101/2020.11.24.396820 fatcat:nwafrwbuwzedfl4j7xbnrs3y24

Phylogenetic Quantification of Intratumor Heterogeneity

Thomas B.K. Watkins, Roland F. Schwarz
2017 Cold Spring Harbor Perspectives in Medicine  
As sequencing efforts continue to reveal the extent of the intratumor heterogeneity (ITH) present in human cancers, the importance of evolutionary studies attempting to trace its etiology has increased  ...  We describe how multiple samples can guide tree inference through accurate phasing of germline variants and copy-number profiles.  ...  Large-scale collections of cancer studies, such as The Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC), largely consist of pairs of primary tumor and matched normal samples  ... 
doi:10.1101/cshperspect.a028316 pmid:28710259 fatcat:vm3fexo6dbfejpgmklo3kysngy

Early high rates and disparity in the evolution of ichthyosaurs

Benjamin C. Moon, Thomas L. Stubbs
2020 Communications Biology  
Using recent cladistic data, skull length data, and the most complete phylogenetic trees to date for the group, we present a combined disparity, morphospace, and evolutionary rates analysis that reveals  ...  the tempo and mode of ichthyosaur morphological evolution through 160 million years.  ...  Received: 11 October 2019; Accepted: 7 January 2020; Acknowledgements The authors are very grateful to Armin Elsler (University of Bristol) for sharing R code that greatly improved the efficiency of  ... 
doi:10.1038/s42003-020-0779-6 pmid:32054967 fatcat:47wkxh6q2fhnfap3zqcc7p7jda

Evolution of human-competitive lossless compression algorithms with GP-zip2

Ahmed Kattan, Riccardo Poli
2011 Genetic Programming and Evolvable Machines  
in heterogeneous archive files.  ...  Experimentation shows that the results produced by GP-zip2 are human-competitive, being typically superior to well-established human-designed compression algorithms in terms of the compression ratios achieved  ...  To avoid pathologies of this kind, the system verifies whether the splitter tree has found a sufficiently large number of blocks.  ... 
doi:10.1007/s10710-011-9133-6 fatcat:zsczdrzljjdqvbowdujo6lbyk4

Genomes reveal drastic and recurrent phenotypic divergence in firetip skipper butterflies (Hesperiidae: Pyrrhopyginae)

Jing Zhang, Qian Cong, Jinhui Shen, Ernst Brockmann, Nick V. Grishin
2019 Proceedings of the Royal Society of London. Biological Sciences  
Genomic analysis promises to elucidate evolutionary relationships and shed light on molecular mechanisms of divergence.  ...  These differences (in particular, a transition between unspotted black and striped wings) happen recurrently on a short evolutionary time scale, and are therefore probably achieved by a small number of  ...  study, which has been supported by the grants from the National Institutes of Health GM094575 and GM127390 and the Welch Foundation I-1505.  ... 
doi:10.1098/rspb.2019.0609 pmid:31113329 pmcid:PMC6545083 fatcat:zbd56a5zazbmbp5nhc4xsfzioq

Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough

Hervé Philippe, Henner Brinkmann, Dennis V. Lavrov, D. Timothy J. Littlewood, Michael Manuel, Gert Wörheide, Denis Baurain, David Penny
2011 PLoS Biology  
Speciations compressed in time and large reproductive populations both increase the likelihood of this phenomenon.  ...  With such models, only the evolutionary rate can be modeled as heterogeneous across sites, usually through a gamma distribution of rates.  ... 
doi:10.1371/journal.pbio.1000602 pmid:21423652 pmcid:PMC3057953 fatcat:qth4lq6qwvflda4jewizcwiykm

Network Big Data: A Literature Survey on Stream Data Mining

Yi Wu
2014 Journal of Software  
With the rapid development of Internet, the internet of things and other information technology, big data usually exists in cyberspace as the form of the data stream.  ...  ACKNOWLEDGMENT This work is supported by the Nature Science Foundation of Heilongjiang Province with the grant number: F201325. The author would like to thank for their support.  ...  Firstly, UDS-FIM maintains probability values of each transactions to an array; secondly, compresses each transaction to a UDS-Tree in the same manner as an FP-Tree (so it is as compact as an FP-Tree)  ... 
doi:10.4304/jsw.9.9.2427-2434 fatcat:u52qdqy3xbd2la5a4m3tklm5c4

A Comparative Wood Anatomy of 15 Woody Species in North-eastern Mexico

Maiti R, Rodriguez HG
2016 Forest Research Open Access  
Rays narrow, long, 2-4 celled, heterogeneous, ray cells non-stratified ( Figure 6 ). Wood arranged in rings, diffuse porous, vessels few, arranged in groups 3 to 5 cells, ovoidal but compressed.  ...  Rays spindle shaped moderately long, maximum 3 to 6 celled in breadth, tapering, heterogeneous, compressed rays spindle shaped, very broad, mutilayered, composed highly compact small round cells, seems  ... 
doi:10.4172/2168-9776.1000166 fatcat:bfzne7wq5vgkzmjmfly4bh7sim

Extreme and rapid bursts of functional adaptations shape bite force in amniotes

Manabu Sakamoto, Marcello Ruta, Chris Venditti
2019 Proceedings of the Royal Society of London. Biological Sciences  
However, ignoring evolutionary history, in particular ancestry, passage of time and the rate of evolution, can be misleading.  ...  Here, we apply a recently developed phylogenetic statistical approach using significant rate shifts to detect instances of exceptional rates of adaptive changes in bite force in a large group of terrestrial  ...  Our hypothesis specifically concerns exceptional rates of adaptive changes and not rate heterogeneity-exceptional rates of adaptation is defined as instances of exceptionally large rate increases (at least  ... 
doi:10.1098/rspb.2018.1932 pmid:30963871 pmcid:PMC6367170 fatcat:brhhwjfkyjdh7kxhz22hemyboi
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