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Bosque specifications


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




No version available


  • person_outline Salvador Ramírez-Flandes <>

Publication for Bosque

Bosque citations


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

PMCID: 4490794
PMID: 26191046
DOI: 10.3389/fmicb.2015.00638

[…] 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, ramírez-flandes and ulloa, ). sequence data were analyzed with the arb software package (ludwig et al., ) and phylogenetic reconstruction was performed […]


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

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

[…] new nucleotide sequences and their motu (molecular operational taxonomic unit) assignments are available under accession numbers hf559482-hf560561., 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 […]


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

PMCID: 3119654
PMID: 21713028
DOI: 10.1371/journal.pbio.1001085

[…] 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., hek293 cells (health protection agency culture collection, salisbury, uk) […]


Nitrogen Fixation in Denitrified Marine Waters

PMCID: 3110191
PMID: 21687726
DOI: 10.1371/journal.pone.0020539

[…] 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 […]

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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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