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SwissTree specifications

Information


Unique identifier OMICS_20827
Name SwissTree
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Maintained Yes

Maintainer


  • person_outline Brigitte Boeckmann

Publication for SwissTree

SwissTree citations

 (3)
library_books

GATC: a genetic algorithm for gene tree construction under the Duplication Transfer Loss model of evolution

2018
BMC Genomics
PMCID: 5954287
PMID: 29764363
DOI: 10.1186/s12864-018-4455-x

[…] ) and the V-type ATPase beta subunit (VATP).These gene families have been re-analyzed here to assess the performance of GATC on an empirical dataset. The reference species tree used was obtained from SwissTree []. Protein sequences from genomes not found in the species tree were removed and the remaining sequences aligned with Muscle []. GATC was used to reconstruct the corresponding trees for eac […]

library_books

Towards Consensus Gene Ages

2016
Genome Biol Evol
PMCID: 4943184
PMID: 27259914
DOI: 10.1093/gbe/evw113

[…] We inferred the ages for each gene by mapping the species in that gene’s ortholog group onto a reference species tree from SwissTree, which was derived from a consensus of trees found in the literature (). The age of a protein is calculated on the species tree by finding the MRCA node of the taxa that have orthologs of th […]

library_books

Standardised Benchmarking in the Quest for Orthologs

2016
Nat Methods
PMCID: 4827703
PMID: 27043882
DOI: 10.1038/nmeth.3830

[…] anual oversight is expected to yield gene phylogenies with high statistical support and topological consistency.Concordance of orthology predictions was assessed with two sets of trees. The first was SwissTree,, a small collection of large and high-confidence gene family phylogenies with different types of challenges for orthology prediction and species from all domains. The second, TreeFam-A, con […]

Citations

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SwissTree institution(s)
Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland; Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland; Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland; SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland; Vital-IT, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland; Evolutionary Bioinformatics group, Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland; Department of Computer Science, ETH Zurich, Zurich, Switzerland; SIB Swiss Institute of Bioinformatics, Zurich, Switzerland; Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland; SIB Swiss Institute of Bioinformatics, Geneva, Switzerland; University of Geneva, Department of Biochemistry, Geneva, Switzerland; Department of Evolutionary and Environmental Biology, Institute of Evolution, University of Haifa, Haifa, Israel; Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain; Department of Genetics Evolution and Environment, University College London, London, UK; Department of Computer Science, University College London, London, UK
SwissTree funding source(s)
Supported by the Swiss State Secretariat for Education, Research and Innovation (SERI) funding; Swiss National Science Foundation grant 150654; and by the Swiss Institute of Bioinformatics

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