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Model checking software for phylogenetic trees using distribution and database methods
2013
Journal of Integrative Bioinformatics
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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. ...
This strategy allows us to use generic software tools already present in the industry. ...
Section 3 introduces the adaptation and implementation of distributed model checking techniques for the particular case of phylogenetic trees. ...
doi:10.2390/biecoll-jib-2013-229
pmid:24231143
fatcat:xslrev5pbvebjd3clfyugb6joq
An Approach to the Identification and Phylogenetic Analysis of Emerging and Hemorrhagic Fever Viruses
[chapter]
2017
Msphere
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Directed surveillance for viruses of a specific taxonomic group provides the investigator with sequence files from cDNA amplified using specific primers to conserved viral regions. ...
Here we will describe general approaches to identify hemorrhagic viral agents through phylogenetic analysis of cDNA sequences obtained during surveillance activities. ...
Materials Besides the sequences, the only other "materials" required for phylogenetic sequence analyses are the appropriate computer hardware and software: a sequence database and one or more phylogenetic ...
doi:10.1007/978-1-4939-6981-4_2
pmid:28986823
fatcat:s2gd72qvwrg5dpsyywry5qi6d4
The Generation Challenge Programme comparative plant stress-responsive gene catalogue
2007
Nucleic Acids Research
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This public resource is a compendium of protein families, phylogenetic trees, multiple sequence alignments (MSA) and associated experimental evidence. ...
The web-based graphical user interface (GUI) of the resource includes query and visualization tools that allow diverse searches and browsing of the underlying project database. ...
ACKNOWLEDGEMENTS Funding to pay the Open Access publication charges for this article was provided by Generation Challenge Programme. ...
doi:10.1093/nar/gkm798
pmid:17933772
pmcid:PMC2238985
fatcat:tczhxtfxcfe3hh635v7xybrmy4
PhySpeTree: an automated pipeline for reconstructing phylogenetic species trees
2019
BMC Evolutionary Biology
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Together with accessory modules, PhySpeTree significantly simplifies tree reconstruction. PhySpeTree is implemented in Python running on modern operating systems (Linux, macOS, and Windows). ...
Acknowledgements We thank Yaodong Liu for testing PhySpeTree. ...
This module is useful for comparing and selecting conserved branches from trees generated by different sequences or tree building methods. ...
doi:10.1186/s12862-019-1541-x
pmid:31791235
pmcid:PMC6889546
fatcat:7g57bkn6sfe4fh2jv2h25vwqiy
Applied aspects of methods to infer phylogenetic relationships amongst fungi
2020
Mycosphere
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This is not at all to elaborate the theoretical background but is intended as a compact guide of some useful software references and coding for the most commonly used phylogenetic methods applied in mycological ...
Meanwhile, necessary steps from DNA extraction to DNA sequencing, sequences quality check, data alignment and general steps of phylogenetic tree reconstructions have been included. ...
Hyde for his valuable suggestions to shape the paper and Dr. Martin Ryberg is thanked for providing comments to improve it. Dhanushka N. Wanasinghe, Chada Norphanphoun and Milan C. ...
doi:10.5943/mycosphere/11/1/18
fatcat:gz6iinpo55debgebotua5idnam
The first two cases of 2019‐nCoV in Italy: where they come from?
2020
Journal of Medical Virology
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Viral genome phylogenetic analysis represents a useful tool for the evaluation of transmission dynamics and preventive action. ...
A maximum clade credibility tree has been built using a dataset of 54 genome sequences of 2019-nCoV plus two closely related bat strains (SARS-like CoV) available in GenBank. ...
The convergence of MCMC chains was checked using Tracer v.1.7.1. 12 Proper mixing of the MCMC was checked for ESS values greater than 200 for each estimated parameter using Tracer 1.7. ...
doi:10.1002/jmv.25699
pmid:32022275
fatcat:o4w2cn5rp5bl3krlfnnhhnglpe
Analyzing phylogenetic trees with timed and probabilistic model checking: the lactose persistence case study
2014
Journal of Integrative Bioinformatics
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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. ...
Besides, model checking allows us to uncouple software tools from the definition of properties and it hides the underlying implementation technology [7] . ...
doi:10.2390/biecoll-jib-2014-248
pmid:25339082
fatcat:m76d54tlsnhhfk7t7b6gwvtu5e
25 years of serving the community with ribosomal RNA gene reference databases and tools
2017
Journal of Biotechnology
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Wolfgang Ludwig from the Technical University Munich started the integrated software workbench ARB (lat. tree) to support high-quality phylogenetic inference and taxonomy based on the SSU and LSU rDNA ...
At that time, the ARB project maintained both, the sequence reference datasets and the software package for data analysis. ...
Your immediate critical evaluation is a great motivation for us to improve our databases and tools. ...
doi:10.1016/j.jbiotec.2017.06.1198
pmid:28648396
fatcat:u35qpimwazhhnip774tn433bha
Analyzing Phylogenetic Trees with Timed and Probabilistic Model Checking: The Lactose Persistence Case Study
2014
Journal of Integrative Bioinformatics
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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. ...
Besides, model checking allows us to uncouple software tools from the definition of properties and it hides the underlying implementation technology [7] . ...
doi:10.1515/jib-2014-248
fatcat:c5byw44cvzbqpdbd2krpkv7yua
IMGT/PhyloGene: an on-line tool for comparative analysis of immunoglobulin and T cell receptor genes
2003
Developmental and Comparative Immunology
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IMGT/PhyloGene is the first tool to use the IMGT expertized and standardized data for automated comparative analyses, and the first on-line software package for phylogenetic reconstruction to be integrated ...
to a sequence database. ...
Acknowledgements We are grateful to Véronique Giudicelli, Céline Protat, Denys Chaume and Olivier Gascuel for helpful discussions. ...
doi:10.1016/s0145-305x(03)00078-8
pmid:12818634
fatcat:dpdfjiclibemnnljajlqvdqgty
Syntactic Phylogenetic Trees
[article]
2016
arXiv
pre-print
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In this paper we identify several serious problems that arise in the use of syntactic data from the SSWL database for the purpose of computational phylogenetic reconstruction. ...
This is a promising sign for the use of SSWL data for linguistic phylogenetics. ...
Given the Hamming distance matrix M ab = d H ( a , b ), the PHYLIP software provides several options for tree construction from distance matrix data: additive tree model, ultrametric model, neighbor joining ...
arXiv:1607.02791v1
fatcat:exd7pifh65ctfgmbhk7ii2jcu4
High-resolution and Deep Phylogenetic Reconstruction of Ancestral States from Large Transcriptomic Data Sets
2020
Bio-protocol
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To achieve a correct phylogenetic understanding of genes or proteins, reliable and robust methods are needed to construct meaningful trees. ...
Building meaningful phylogenetic trees is needed for the accurate reconstruction of the past. ...
Efforts of all the authors are highly appreciated, who developed many extremely useful and efficient programs and algorithms for phylogenetics, and making them freely accessible to the scientific community ...
doi:10.21769/bioprotoc.3566
pmid:33659537
pmcid:PMC7842344
fatcat:jp22rmvvgnaivptxpshngyncwe
Building megaphylogenies for macroecology: taking up the challenge
2012
Ecography
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Th e initial discussion around the issue was developed under the ANR DIVERSITALP (ANR-07-BDIV-014) and EVORANGE (ANR-09-PEXT-011) projects. ...
Th is is possible thanks to improved phylogenetic methods, vast amounts of molecular data available from databases such as Genbank, and consensus knowledge on deep phylogenetic relationships for an increasing ...
Growing molecular databases such as Genbank, increased consensus of deep phylogenetic relationships and recent improvements in software (e.g. ...
doi:10.1111/j.1600-0587.2012.07773.x
pmid:24790290
pmcid:PMC4001083
fatcat:q434owsnnzdtnifjliucfxe42y
WOODIV, a database of occurrences, functional traits, and phylogenetic data for all Euro-Mediterranean trees
2021
Scientific Data
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matK, and trnH-psbA), together with modelled occurrences and a phylogeny for all 210 Euro-Mediterranean tree species. ...
Despite its particularities and vulnerability, the biodiversity of Mediterranean trees is not well known at the taxonomic, spatial, functional, and genetic levels required for conservation applications ...
The six missing species for which no DNA-region sequence was available were added to the phylogenetic tree using the Simulation with Uncertainty for Phylogenetic Investigating (SUNPLIN) method 73 , with ...
doi:10.1038/s41597-021-00873-3
pmid:33758194
fatcat:3nrgko257jbcbhxlwzynecgary
PhyloFacts: an online structural phylogenomic encyclopedia for protein functional and structural classification
2006
Genome Biology
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PhyloFacts enables biologists to avoid the systematic errors associated with function prediction by homology through the integration of a variety of experimental data and bioinformatics methods in an evolutionary ...
The Berkeley Phylogenomics Group presents PhyloFacts, a structural phylogenomic encyclopedia containing almost 10,000 'books' for protein families and domains, with pre-calculated structural, functional ...
The authors wish to thank several anonymous reviewers for very helpful comments and suggestions. ...
doi:10.1186/gb-2006-7-9-r83
pmid:16973001
pmcid:PMC1794543
fatcat:uib3z34bjzfcneno7favzrp6ri
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