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Protocols

TreeBASE specifications

Information


Unique identifier OMICS_20671
Name TreeBASE
Restrictions to use Academic or non-commercial use
Database management system PostgreSQL
Community driven No
Data access File download, Browse
User data submission Allowed
Maintained Yes

Documentation


Maintainer


  • person_outline TreeBASE Team

Additional information


https://github.com/TreeBASE/treebase

Publication for TreeBASE

TreeBASE citations

 (888)
library_books

Papain like and legumain like proteases in rice: genome wide identification, comprehensive gene feature characterization and expression analysis

2018
BMC Plant Biol
PMCID: 5952849
PMID: 29764367
DOI: 10.1186/s12870-018-1298-1

[…] onal Genomic Express Database (http://signal.salk.edu/cgi-bin/RiceGE). Protein sequence and phylogeny data, including alignments, have been deposited in the TreeBASE repository (http://purl.org/phylo/treebase/phylows/study/TB2:S22378). […]

call_split

Eight new Arthrinium species from China

2018
PMCID: 5945706
PMID: 29755262
DOI: 10.3897/mycokeys.34.24221
call_split See protocol

[…] ees were used for calculating PP in the majority rule consensus tree. Sequences generated in this study were deposited in GenBank (Table ) and the final matrices used for the phylogenetic analyses in TreeBASE (www.treebase.org; accession number: 21341). […]

library_books

Evolutionary novelty in gravity sensing through horizontal gene transfer and high order protein assembly

2018
PLoS Biol
PMCID: 5915273
PMID: 29689046
DOI: 10.1371/journal.pbio.2004920

[…] th generation for 300,000 generations. Convergence was assessed using RWTY []. The ML and Bayesian phylogenies, as well as the matrix used to derive them are accessible under the identifier S22330 at TreeBASE (https://treebase.org/). To compare the ML trees with and without the monophyly constraint, the best-scoring tree with monophyly constraint was constructed using RAxML with the same parameter […]

call_split

Testing the impact of effective population size on speciation rates – a negative correlation or lack thereof in lichenized fungi

2018
Sci Rep
PMCID: 5893563
PMID: 29636516
DOI: 10.1038/s41598-018-24120-9
call_split See protocol

[…] al transcribed spacer region (ITS) sequences from Xanthoparmelia (n = 198), Melanohalea (489), Melanelixia (264), and their close relatives, Montanelia (60) and Emodomelanelia (2), were obtained from TreeBase (S11457 & S18577). A previous species delimitation and taxonomic study of Melanelixia and Melanohalea was based on sampling of worldwide populations, and approximately 20% of species in these […]

library_books

First molecular detection and characterization of Marek’s disease virus in red crowned cranes (Grus japonensis): a case report

2018
PMCID: 5883596
PMID: 29615025
DOI: 10.1186/s12917-018-1437-9

[…] The datasets analysed during the current study are available in the TreeBASE repository. Our data are posted as NEXUS files in the following public domain resources: http://purl.org/phylo/treebase/phylows/study/TB2:S22355. The viral protein sequences of different MDV strains were deposited in GenBank under the accession number in Tables , and . […]

library_books

Comparison of taxon‐specific versus general locus sets for targeted sequence capture in plant phylogenomics

2018
Appl Plant Sci
PMCID: 5895190
PMID: 29732262
DOI: 10.1002/aps3.1032

[…] e general locus sets. Concatenated alignments for each locus set are available in the Dryad Digital Repository (https://doi.org/10.5061/dryad.v6q0p; Chau et al., ) and TreeBASE (http://purl.org/phylo/treebase/phylows/study/TB2:S21931). […]

Citations

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TreeBASE institution(s)
Institute of Evolutionary and Ecological Sciences, Leiden University, Netherlands; Naturalis Nationaal NatuurHistorisch Museum, Leiden, Netherlands; Harvard University Herbaria, Cambridge, MA, USA; Section of Evolution and Ecology, University of California, Davis, CA, USA
TreeBASE funding source(s)
Supported by Harvard University Herbaria; University of California at Davis; and a SGER NSF grant (DEB9318325).

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