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Bosque specifications

Information


Unique identifier OMICS_15697
Name Bosque
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Database management system SQLite
Computer skills Medium
Version 2.0.2
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Salvador Ramírez-Flandes

Publication for Bosque

Bosque citations

 (6)
call_split

The hydrological context determines the beta diversity of aerobic anoxygenic phototrophic bacteria in European Arctic seas but does not favor endemism

2015
Front Microbiol
PMCID: 4490794
PMID: 26191046
DOI: 10.3389/fmicb.2015.00638
call_split See protocol

[…] rlsbad, CA). Sequences were manually curated, subjected to BLAST search against publicly available sequences, grouped into Operational Taxonomic Units (OTUs) according to a cut-off value of 94% using BOSQUE (available at http://bosque.udec.cl, Ramírez-Flandes and Ulloa, ). Sequence data were analyzed with the ARB software package (Ludwig et al., ) and phylogenetic reconstruction was performed as d […]

library_books

Paralia (Bacillariophyta) stowaways in ship ballast: implications for biogeography and diversity of the genus

2015
PMCID: 4389653
PMID: 25984507
DOI: 10.1186/s40709-015-0024-5

[…] ise Kimura-2-Parameter (K2P) model. Maximum parsimony (MP) trees were generated by close-neighbour-interchange (CNI) on random trees. For Maximum Likelihood (ML) trees, jModeltest version 0.1.1 [] in Bosque [] was used to select optimal base substitution models according to Akaike Information Criterion (AIC). The Hasegawa, Kishino and Yano (HKY) + Gamma (G) model (−ln L = 1033.68) and the Generali […]

library_books

Network Analysis Reveals Ecological Links between N Fixing Bacteria and Wood Decaying Fungi

2014
PLoS One
PMCID: 3914916
PMID: 24505405
DOI: 10.1371/journal.pone.0088141

[…] We have obtained, through importing into BOSQUE v. 1.81. , the GenBank flatfiles of all nucleic acid accession numbers contained in the ARB database provided online by the Zehr Marine Microbiology lab, University of California at Santa Cruz […]

library_books

Intraspecific Variation of the Aquatic Fungus Articulospora tetracladia: An Ubiquitous Perspective

2012
PLoS One
PMCID: 3338785
PMID: 22558256
DOI: 10.1371/journal.pone.0035884

[…] using MEGA 4 . All positions containing alignment gaps and missing data were eliminated only in pairwise sequence comparisons. Branch support was determined with bootstrap analysis (1000 replicates).Bosque was used for analyzing ITS1-5.8S-ITS2 to determine the operational taxonomic units (OTUs) from the similarity table (similarity % = 100). Arlequin 3.5.1.2 was employed to analyse the OTUs to […]

call_split

A Voltage Gated H+ Channel Underlying pH Homeostasis in Calcifying Coccolithophores

2011
PLoS Biol
PMCID: 3119654
PMID: 21713028
DOI: 10.1371/journal.pbio.1001085
call_split See protocol

[…] mains. Sequences were aligned using MUSCLE and then manually corrected to ensure only unambiguous residues were compared. Maximum likelihood phylogenetic analysis was performed using PhyML within the Bosque software package , based on the JTT substitution matrix . One hundred bootstrap replicates were performed. […]

call_split

Nitrogen Fixation in Denitrified Marine Waters

2011
PLoS One
PMCID: 3110191
PMID: 21687726
DOI: 10.1371/journal.pone.0020539
call_split See protocol

[…] trees. Sequence alignment in the amino acid space was performed with MUSCLE 3.6 . The maximum-likelihood phylogenetic tree in was constructed with PhyML using the default parameters in the program Bosque . Percentages of Bootstrap support values (≥50) based on 1000 replications are shown at the nodes. Sequence data were deposited in the GenBank database under accession numbers HM801148 to HM801 […]

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Bosque institution(s)
Departmento de Oceanografía, Universidad de Concepción, Concepción, Chile
Bosque funding source(s)
This work was supported by the Chilean National Commission for Scientific and Technological Research through the PBCT (grant RED12), FONDAP (grant 15010007) programs, and the Millennium Scientific Initiative (grant EBMA P04/007).

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