Filters








19,589 Hits in 5.8 sec

MetaPhOrs: orthology and paralogy predictions from multiple phylogenetic evidence using a consistency-based confidence score

Leszek P. Pryszcz, Jaime Huerta-Cepas, Toni Gabaldón
2010 Nucleic Acids Research  
This provides us with the opportunity to infer the evolutionary relationships of genes from multiple, independent, phylogenetic trees.  ...  Using such strategy, we combine phylogenetic information derived from different databases, to predict orthology and paralogy relationships for 4.1 million proteins in 829 fully sequenced genomes.  ...  ACKNOWLEDGEMENTS The authors want to acknowledge Diego Kormes and Salvador Capella-Gutı´errez for their help with phylogenetic reconstruction of EggNOG, OrthoMCL and COG families.  ... 
doi:10.1093/nar/gkq953 pmid:21149260 pmcid:PMC3061081 fatcat:mfp625j4lngb7ktfgbajdqn2va

MetaPhOrs 2.0: integrative, phylogeny-based inference of orthology and paralogy across the tree of life

Uciel Chorostecki, Manuel Molina, Leszek P Pryszcz, Toni Gabaldón
2020 Nucleic Acids Research  
Inferring homology relationships across genes in different species is a central task in comparative genomics. Therefore, a large number of resources and methods have been developed over the years.  ...  Some public databases include phylogenetic trees of homologous gene families which can be used to further differentiate homology relationships into orthology and paralogy.  ...  METAPHORS WEB SERVER DESCRIPTION MetaPhOrs is a public repository of phylogeny-based orthologs and paralogs that were computed using phylogenetic trees available in several repositories.  ... 
doi:10.1093/nar/gkaa282 pmid:32343307 fatcat:hkc5mjymwng4jpkeczmylztu6m

CDAOStore: A Phylogenetic Repository Using Logic Programming and Web Services

Brandon Chisham, Enrico Pontelli, Tran Cao Son, Ben Wright, Marc Herbstritt
2011 International Conference on Logic Programming  
The CDAOStore is a portal aimed at facilitating the storage and retrieval of data and metadata associated to studies in the field of evolutionary biology and phylogenetic analysis.  ...  The novelty of CDAOStore lies in the use of a semantic-based approach to the storage and querying of data.  ...  Background Phylogenetics and Interoperation: Phylogenetic trees (a.k.a. phylogenies) have gained a central role in modern biology.  ... 
doi:10.4230/lipics.iclp.2011.209 dblp:conf/iclp/ChishamPSW11 fatcat:yqmnsx3zz5fsjlyjodho5mpkue

PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions

J. Huerta-Cepas, S. Capella-Gutierrez, L. P. Pryszcz, I. Denisov, D. Kormes, M. Marcet-Houben, T. Gabaldon
2010 Nucleic Acids Research  
Currently, PhylomeDB is the largest phylogenetic repository and hosts 17 phylomes, comprising 416 093 trees and 165 840 alignments.  ...  For each protein-coding gene in a seed genome, the database provides original and processed alignments, phylogenetic trees derived from various methods and phylogeny-based predictions of orthology and  ...  Currently, a number of public repositories for automatically-generated collections of phylogenetic trees do exist (6) (7) (8) (9) (10) .  ... 
doi:10.1093/nar/gkq1109 pmid:21075798 pmcid:PMC3013701 fatcat:3tcb5kxz7jh45clzzjrmysdvhm

Crimson: A Data Management System to Support Evaluating Phylogenetic Tree Reconstruction Algorithms

Yifeng Zheng, Stephen Fisher, Shirley Cohen, Sheng Guo, Junhyong Kim, Susan B. Davidson
2006 Very Large Data Bases Conference  
Although much attention has been focused on XML as a tree data model, phylogenetic trees differ from document-oriented applications in their size and depth, and their need for structurebased queries rather  ...  Evolutionary and systems biology increasingly rely on the construction of large phylogenetic trees which represent the relationships between species of interest.  ...  between nodes in a layer 1 tree is the same as the relationship between the subtrees in layer 0.  ... 
dblp:conf/vldb/ZhengFCGKD06 fatcat:gm34um4v7jfhloauhem2s6ikhu

Synthesis of phylogeny and taxonomy into a comprehensive tree of life

Cody E. Hinchliff, Stephen A. Smith, James F. Allman, J. Gordon Burleigh, Ruchi Chaudhary, Lyndon M. Coghill, Keith A. Crandall, Jiabin Deng, Bryan T. Drew, Romina Gazis, Karl Gude, David S. Hibbett (+10 others)
2015 Proceedings of the National Academy of Sciences of the United States of America  
Reconstructing the phylogenetic relationships that unite all lineages (the tree of life) is a grand challenge.  ...  Input Data: Phylogenetic Trees. We designed and developed a user interface that saves phylogenetic trees directly into a GitHub repository (49) and used this interface to import and curate trees.  ... 
doi:10.1073/pnas.1423041112 pmid:26385966 pmcid:PMC4611642 fatcat:3cvqy4mrhjexhofya2pmbilhcm

CDAO-Store: Ontology-driven Data Integration for Phylogenetic Analysis

Brandon Chisham, Ben Wright, Trung Le, Tran Son, Enrico Pontelli
2011 BMC Bioinformatics  
of data and transformations commonly found in the domain of phylogenetic analysis.  ...  In addition, CDAO-Store provides a visualization front-end, called CDAO-Explorer, which can be used to view both character data matrices and trees extracted from the CDAO-Store.  ...  The National Evolutionary Synthesis Center (NESCent) was instrumental in the development of CDAO and in inspiring this project.  ... 
doi:10.1186/1471-2105-12-98 pmid:21496247 pmcid:PMC3101187 fatcat:f2xokjd6c5daporl5albcevica

Phylogenomic Analyses of Echinodermata Support the Sister Groups of Asterozoa and Echinozoa

Adrian Reich, Casey Dunn, Koji Akasaka, Gary Wessel, Hector Escriva
2015 PLoS ONE  
Using multiple phylogenetic methods at a variety of sampling depths we have constructed a wellsupported phylogenetic tree of Echinodermata, including support for the sister groups of Asterozoa (sea stars  ...  In order to test echinoderm phylogenetic relationships, we sequenced 23 de novo transcriptomes from all five clades of echinoderms.  ...  In order to compare one a priori tree with the maximum likelihood RAxML tree generated from this dataset, the parametric SOWH can avoid any selection bias and is more appropriate [38] .  ... 
doi:10.1371/journal.pone.0119627 pmid:25794146 pmcid:PMC4368666 fatcat:i57namrlpfaqdjfmg3bqrjlsqy

Phylesystem: a git-based data store for community curated phylogenetic estimates [article]

Emily Jane B. McTavish, Cody E. Hinchliff, James F. Allman, Joseph W. Brown, Karen A. Cranston, Mark T. Holder, Jonathan A. Rees, Stephen A. Smith
2015 bioRxiv   pre-print
Furthermore, establishing the mapping between tip labels used in a tree and taxa in a single common taxonomy dramatically improves the ability of other researchers to reuse phylogenetic estimates.  ...  Such services fulfill a crucial role in ensuring transparency and reproducibility in phylogenetic research.  ...  Jonathan "Duke" Leto wrote some of the code for a preliminary version of the phylesystem-api tool which served as the initial code base for the current implementation.  ... 
doi:10.1101/013862 fatcat:jejnnmktnfhd5gypxbihwp6zyy

PhylomeDB V5: an expanding repository for genome-wide catalogues of annotated gene phylogenies

Diego Fuentes, Manuel Molina, Uciel Chorostecki, Salvador Capella-Gutiérrez, Marina Marcet-Houben, Toni Gabaldón
2021 Nucleic Acids Research  
This release also represents a significant core data expansion, with the database providing access to 534 phylomes, comprising over 8 million trees, and homology relationships for genes in over 6000 species  ...  In addition, PhylomeDB trees and alignments can be downloaded for further processing to detect and date gene duplication events, infer past events of inter-species hybridization and horizontal gene transfer  ...  PhylomeDB (Phylome database) is a knowledgebase of evolutionary relationships between protein-coding genes, represented in the form of annotated phylogenetic trees and multiple sequence alignments, which  ... 
doi:10.1093/nar/gkab966 pmid:34718760 pmcid:PMC8728271 fatcat:ju54alsn3nhozencrsbxmbhjbe

Phylomatic: tree assembly for applied phylogenetics

CAMPBELL O. WEBB, MICHAEL J. DONOGHUE
2005 Molecular Ecology Notes  
which returns a phylogenetic hypothesis for the relationships among taxa.  ...  Any set of stored phylogenies, or a user-supplied one, can be chosen as the basis for the returned phylogeny, and several output formats for the tree can be selected.  ...  Overall, we feel that all areas of biology can benefit from a move away from treating taxa as independent entities and toward recognizing explicit relationships in the tree of life.  ... 
doi:10.1111/j.1471-8286.2004.00829.x fatcat:cmt5vzp52zfuznjizvjqmhqp6m

Phylesystem: a git-based data store for community-curated phylogenetic estimates: Fig. 1

Emily Jane McTavish, Cody E. Hinchliff, James F. Allman, Joseph W. Brown, Karen A. Cranston, Mark T. Holder, Jonathan A. Rees, Stephen A. Smith
2015 Bioinformatics  
Furthermore, establishing the mapping between tip labels used in a tree and taxa in a single common taxonomy dramatically improves the ability of other researchers to reuse phylogenetic estimates.  ...  Such services fulfill a crucial role in ensuring transparency and reproducibility in phylogenetic research.  ...  Jonathan 'Duke' Leto wrote some of the code for a preliminary version of the phylesystem-api tool which served as the initial code base for the current implementation.  ... 
doi:10.1093/bioinformatics/btv276 pmid:25940563 pmcid:PMC4547614 fatcat:5eq2clzypbei5ledpnd6ljdrgq

BIO-AJAX

Katherine G. Herbert, Narain H. Gehani, William H. Piel, Jason T. L. Wang, Cathy H. Wu
2004 SIGMOD record  
This paper proposes one such framework, called BIO-AJAX, which uses principles from data cleaning to improve data quality in biological information systems, specifically in TreeBASE.  ...  In the case of these trees, each tree studies evolutionary relationships between specific organisms within the species.  ...  For example, there are a number of algorithms that can perform matching in any data set, including phylogenetic trees.  ... 
doi:10.1145/1024694.1024703 fatcat:te3ykc7wrvdcjdpygmsuiy757e

Treebase: an R package for discovery, access and manipulation of online phylogenies

Carl Boettiger, Duncan Temple Lang, Luke Harmon
2012 Methods in Ecology and Evolution  
data in the TreeBASE repository. 3.  ...  The R statistical environment has also become a primary tool for applied phylogenetic analyses across a range of questions, from comparative evolution to community ecology to conservation planning. 2.  ...  Price for feedback on the manuscript, the TreeBASE developer team for building and supporting the repository, and all contributors to TreeBASE.  ... 
doi:10.1111/j.2041-210x.2012.00247.x fatcat:yyzdktbe6ja5tjtvtrrrw3lany

A Target Enrichment Method for Gathering Phylogenetic Information from Hundreds of Loci: An Example from the Compositae

Jennifer R. Mandel, Rebecca B. Dikow, Vicki A. Funk, Rishi R. Masalia, S. Evan Staton, Alex Kozik, Richard W. Michelmore, Loren H. Rieseberg, John M. Burke
2014 Applications in Plant Sciences  
Data matrices and phylogenetic trees have been deposited in the Dryad Data Repository (http://doi.org/10.5061/dryad.gr93t; Mandel et al., 2014 ) .  ...  A broader study of the phylogenetic relationships within the Compositae using this method and their relationship with chloroplast loci is underway (Mandel et al., in prep) .  ... 
doi:10.3732/apps.1300085 pmid:25202605 pmcid:PMC4103609 fatcat:5vfj5k7fsrc45falfvcljn6lia
« Previous Showing results 1 — 15 out of 19,589 results