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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 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]

Francisco J. Díaz, Luis E. Paternina, Juan David Rodas
2017 Msphere  
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

Samart Wanchana, Supat Thongjuea, Victor Jun Ulat, Mylah Anacleto, Ramil Mauleon, Matthieu Conte, Mathieu Rouard, Manuel Ruiz, Nandini Krishnamurthy, Kimmen Sjolander, Theo van Hintum, Richard M. Bruskiewich
2007 Nucleic Acids Research  
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

Yang Fang, Chengcheng Liu, Jiangyi Lin, Xufeng Li, Kambiz N Alavian, Yi Yang, Yulong Niu
2019 BMC Evolutionary Biology  
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

AJ Dissanayake
2020 Mycosphere  
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?

Marta Giovanetti, Domenico Benvenuto, Silvia Angeletti, Massimo Ciccozzi
2020 Journal of Medical Virology  
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

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.  ...  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

Frank Oliver Glöckner, Pelin Yilmaz, Christian Quast, Jan Gerken, Alan Beccati, Andreea Ciuprina, Gerrit Bruns, Pablo Yarza, Jörg Peplies, Ralf Westram, Wolfgang Ludwig
2017 Journal of Biotechnology  
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

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.  ...  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

Olivier Elemento, Marie-Paule Lefranc
2003 Developmental and Comparative Immunology  
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]

Kevin Shu, Sharjeel Aziz, Vy-Luan Huynh, David Warrick, Matilde Marcolli
2016 arXiv   pre-print
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

Sumanth Mutte, Dolf Weijers
2020 Bio-protocol  
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

Cristina Roquet, Wilfried Thuiller, Sébastien Lavergne
2012 Ecography  
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

Anne-Christine Monnet, Kévin Cilleros, Frédéric Médail, Marwan Cheikh Albassatneh, Juan Arroyo, Gianluigi Bacchetta, Francesca Bagnoli, Zoltán Barina, Manuel Cartereau, Nicolas Casajus, Panayotis Dimopoulos, Gianniantonio Domina (+14 others)
2021 Scientific Data  
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

Nandini Krishnamurthy, Duncan P Brown, Dan Kirshner, Kimmen Sjölander
2006 Genome Biology  
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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