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Model checking software for phylogenetic trees using distribution and database methods

José Ignacio Requeno, José Manuel Colom
2013 Journal of Integrative Bioinformatics  
The first one consists of partitioning the phylogenetic tree into a set of subgraphs each one representing a subproblem to be verified so as to speed up the computation time and distribute the memory consumption  ...  The integration of all these approaches outperforms the results of monolithic model checking and helps us to execute the verification of properties in a real phylogenetic tree.  ...  Depending on the number of formulas and slices, we obtain a higher speed up from the distribution.  ... 
doi:10.2390/biecoll-jib-2013-229 pmid:24231143 fatcat:xslrev5pbvebjd3clfyugb6joq

Page 194 of Functional Ecology Vol. 15, Issue 2 [page]

2001 Functional Ecology  
Vanhooydonck E Oo ® ® a n 3 £ x oO E S ° aod Contrasts log,;, maximal speed were used to simulate evolution of speed, mass and temperature, assuming Brownian motion as the model of evolutionary change.  ...  (b) Phylogenetic analysis, using independent contrasts of body mass and sprint speed. use, and foraging mode).  ... 

PhyloBayes MPI: Phylogenetic Reconstruction with Infinite Mixtures of Profiles in a Parallel Environment

Nicolas Lartillot, Nicolas Rodrigue, Daniel Stubbs, Jacques Richer
2013 Systematic Biology  
The implementation shows close to linear gains in computational speed for up to 64 cores, thus allowing faster phylogenetic reconstruction under complex mixture models.  ...  [Bayesian inference; Dirichlet process; mixture models; phylogenetics; phylogenomics.]  ...  The implementation shows close to linear gains in computational speed for up to 64 cores, thus allowing faster phylogenetic reconstruction under complex mixture models.  ... 
doi:10.1093/sysbio/syt022 pmid:23564032 fatcat:uminwpp6inhvvob6aiqegjy4g4

Analyzing phylogenetic trees with timed and probabilistic model checking: the lactose persistence case study

José Ignacio Requeno, José Manuel Colom
2014 Journal of Integrative Bioinformatics  
Model checking is a generic verification technique that allows the phylogeneticist to focus on models and specifications instead of on implementation issues.  ...  The aim of this paper is to extend the application of model checking techniques beyond qualitative phylogenetic properties and adapt the existing logical extensions and tools to the field of phylogeny.  ...  We have created random phylogenetic trees of up to 1000 tips with a Yule speciation model [33] .  ... 
doi:10.2390/biecoll-jib-2014-248 pmid:25339082 fatcat:m76d54tlsnhhfk7t7b6gwvtu5e

Analyzing Phylogenetic Trees with Timed and Probabilistic Model Checking: The Lactose Persistence Case Study

José Ignacio Requeno, José Manuel Colom
2014 Journal of Integrative Bioinformatics  
The aim of this paper is to extend the application of model checking techniques beyond qualitative phylogenetic properties and adapt the existing logical extensions and tools to the field of phylogeny.  ...  SummaryModel checking is a generic verification technique that allows the phylogeneticist to focus on models and specifications instead of on implementation issues.  ...  We have created random phylogenetic trees of up to 1000 tips with a Yule speciation model [33] .  ... 
doi:10.1515/jib-2014-248 fatcat:c5byw44cvzbqpdbd2krpkv7yua

Flight Speeds among Bird Species: Allometric and Phylogenetic Effects

Thomas Alerstam, Mikael Rosén, Johan Bäckman, Per G. P Ericson, Olof Hellgren, Ben Sheldon
2007 PLoS Biology  
Citation: Alerstam T, Rosén M, Bäckman J, Ericson PGP, Hellgren O (2007) Flight speeds among bird species: Allometric and phylogenetic effects. PLoS Biol 5(8): e197.  ...  Scaling exponents in relation to mass and wing loading were significantly smaller than predicted (about 0.12 and 0.32, respectively, with similar results for analyses based on species and independent phylogenetic  ...  PGPE constructed the phylogenetic tree and classified the species into main phylogenetic groups, and OH performed the scaling analyses based on phylogenetic contrast data.  ... 
doi:10.1371/journal.pbio.0050197 pmid:17645390 pmcid:PMC1914071 fatcat:bcnhae7ud5df5hjqfaycz3szkm

MIRAGE: a functional genomics-based approach for metabolic network model reconstruction and its application to cyanobacteria networks

Edward Vitkin, Tomer Shlomi
2012 Genome Biology  
The reconstructed network models are supplied via standard SBML files.  ...  Then, it is applied to reconstruct genome-scale metabolic network models for 36 sequenced cyanobacteria amenable for constraintbased modeling analysis and specifically for metabolic engineering.  ...  The first speed-up involved the utilization of flux distributions computed in one call to the model consistency check procedure in subsequent calls to this procedure (testing the potential removal of subsequent  ... 
doi:10.1186/gb-2012-13-11-r111 pmid:23194418 pmcid:PMC4053740 fatcat:rra27u75vbawdk2wdoxhg6z7de

A Linear-Time Algorithm for Gaussian and Non-Gaussian Trait Evolution Models

Lam si Tung Ho, Cécile Ané
2014 Systematic Biology  
The computational gain opens up new avenues for complex models or extensive resampling procedures on very large trees.  ...  possibly varying selection parameters along the tree; as well as non-Gaussian models such as phylogenetic logistic regression, phylogenetic Poisson regression, and phylogenetic generalized linear mixed  ...  Our algorithm can be used to speed up parameter estimation and likelihood calculation of trait data under modified BM models like Pagel's lambda, kappa, delta, and the early-burst model (as can also be  ... 
doi:10.1093/sysbio/syu005 pmid:24500037 fatcat:cfnlhexphbh3xamriesq2y4ixm

Grid selection of models of nucleotide substitution

Marta Loureiro, Miguel Pan, Manuel Rodríguez-Pascual, David Posada, Rafael Mayo
2010 Studies in Health Technology and Informatics  
jModelTest is a Java program for the statistical selection of models of nucleotide substitution with thousands of users around the world.  ...  Under the ideal situation, without additional jobs in the cluster so all the 88 jobs ran in parallel, the speed-up was 18.09 (limited by the execution time of the most consuming model calculation).  ...  An essential step of the phylogenetic analysis is the selection of appropriate models of nucleotide substitution [1] .  ... 
pmid:20543444 pmcid:PMC4961237 fatcat:rrvodjnqrbcftnbtfnetw23j5m

An Efficient Parallel Algorithm for Ultrametric Tree Construction Based on 3PR [chapter]

Kun-Ming Yu, Jiayi Zhou, Chun-Yuan Lin, Chuan Yi Tang
2006 Lecture Notes in Computer Science  
One of popular model is ultrametric tree, and it assumed the evolution rate is constant. UPGMA is one of well-known ultrametric tree algorithm.  ...  In the computational biology and taxonomy, to construct phylogenetic tree is an important problem.  ...  Figure 4 is the speed-up ratio of HMDNA data set. We observed that the speed-up ratio of 3PR is better than it without 3PR.  ... 
doi:10.1007/11942634_23 fatcat:p7a37ihqzzeh3p7g2yw6j2wlz4

RibAlign: a software tool and database for eubacterial phylogeny based on concatenated ribosomal protein subunits

Hanno Teeling, Frank Oliver Gloeckner
2006 BMC Bioinformatics  
Up to now, phylogeny based on concatenated ribosomal protein sequences is hampered by the limited set of sequenced genomes and high computational requirements.  ...  In search of an improvement, new phylogenetic methods have been developed alongside with the growing availability of complete genome sequences.  ...  Acknowledgements We thank the Max Planck Society for supporting this work and Marisano James for spell-checking the manuscript and the RibAlign website.  ... 
doi:10.1186/1471-2105-7-66 pmid:16476165 pmcid:PMC1421441 fatcat:uzkvjz2urjeypclcgmtzktdiau

PhyloGrid: a development for a workflow in Phylogeny

Esther Montes, Raul Isea, Rafael Mayo
2010 arXiv   pre-print
The user is able to define the parameters for doing the Bayesian calculation, determine the model of evolution, check the accuracy of the results in the intermediate stages as well as do a multiple alignment  ...  Performance results show there is nearly a linear speed up for the parallel jobs. The same job which originally took two days can be finished within few hours.  ...  They also allow the user to validate the calculations as the phylogenetic tree is being constructed with the help of visual check-outs, so a higher reliability on the final results is expected.  ... 
arXiv:1012.3953v1 fatcat:m7vguzwxoneh7digtj2sbgyvfe

Clade composition of a plant community indicates its phylogenetic diversity

Martin Bitomský, Pavla Mládková, Robin J. Pakeman, Martin Duchoslav
2020 Ecology and Evolution  
The clade indices are promising alternative measures for all projects with a phylogenetic framework, which can trade-off a little precision for a significant speed-up and simplification, such as macroecological  ...  Phylogenetic diversity quantification is based on indices computed from phylogenetic distances among species, which are derived from phylogenetic trees.  ...  in studies where a little precision can be traded-off for significant speed-up and simplification.  ... 
doi:10.1002/ece3.6170 pmid:32313633 pmcid:PMC7160181 fatcat:5553sj5vlbfo3adeglq3osyz6y

Ecomorphological diversification following continental colonization in muroid rodents (Rodentia: Muroidea)

Bader H. Alhajeri, John J. Schenk, Scott J. Steppan
2015 Biological Journal of the Linnean Society  
support of early ecological diversification following the initial colonizations of all continental regions, based on multiple tests, including node height tests, disparity through time plots, evolutionary model  ...  identified with increased diversification rates, not associated with geographical transitions, also did not show patterns of phenotypic divergence predicted by ecological opportunity, which suggests that phylogenetic  ...  (EL2); two speed-ups in the rate of mass evolution ( Fig. 1; MA1 -2), one of which occurred at the same branch as the colonization of South-east Asia (MA1); one speed-up in the rate of evolution of PC1  ... 
doi:10.1111/bij.12695 fatcat:ggxvam74nvas5nknavfq5vc7ia

Building megaphylogenies for macroecology: taking up the challenge

Cristina Roquet, Wilfried Thuiller, Sébastien Lavergne
2012 Ecography  
reduce possible artefacts due to patchy data and speed up the analyses.  ...  Again, conducting BS analyses with a backbone constraint tree will probably help to speed them up and obtain higher supports.  ... 
doi:10.1111/j.1600-0587.2012.07773.x pmid:24790290 pmcid:PMC4001083 fatcat:q434owsnnzdtnifjliucfxe42y
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