Belvu pipeline

Belvu specifications

Information


Unique identifier OMICS_23184
Name Belvu
Software type Application/Script
Interface Graphical user interface
Restrictions to use None
Input format STOCKHOLM,MSF,SELEX,FASTA
Output format STOCKHOLM,MSF,SELEX,FASTA
Operating system Unix/Linux, Mac OS, Windows
License GNU General Public License version 3.0
Computer skills Medium
Version 4.14
Stability Stable
Maintained Yes

Versioning


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Maintainer


  • person_outline Gemma Barson <>

Additional information


http://www.sanger.ac.uk/science/tools/seqtools

Publications for Belvu

Belvu IN pipelines

 (7)
2016
PMCID: 4759884
PMID: 26891798
DOI: 10.1186/s12915-016-0228-7

[…] (hmmer2.0) [69]. the alignment was converted from stockholm to fasta format using bioscripts.convert tools v0.4 (https://pypi.python.org/pypi/bioscripts.convert/0.4). the alignment was examined with belvu program and trimmed to the domain borders. trimmed sequences were then re-aligned with muscle [73]., the evolution of tir_2 domains was inferred with mega5 [74] using the maximum likelihood […]

2015
PMCID: 4432964
PMID: 25924720
DOI: 10.1186/s13059-015-0655-8

[…] and homologous sequences from a jackhmmer search [54]. a non-redundant set of sequences of 90% identity or less was aligned with mafft [55] with default settings. alignments were visualised with belvu [56] and phylogenetic trees constructed using the neighbour-joining method present in belvu using default parameters., additional file 1: , competing interests , the authors declare […]

2015
PMCID: 4432964
PMID: 25924720
DOI: 10.1186/s13059-015-0655-8

[…] of 90% identity or less was aligned with mafft [55] with default settings. alignments were visualised with belvu [56] and phylogenetic trees constructed using the neighbour-joining method present in belvu using default parameters., additional file 1: , competing interests , the authors declare that they have no competing interests., authors’ contributions , ab and ap conceived and designed […]

2014
PMCID: 4263179
PMID: 25566323
DOI: 10.3389/fgene.2014.00439

[…] for each expera domain-containing families were generated independently with the program t-coffee using default parameters (notredame et al., 2000), slightly refined manually and visualized with the belvu program (sonnhammer and hollich, 2005). profiles of the alignment as global hidden markov models (hmms) were generated using hmmer (eddy, 1996; finn et al., 2011). profile-based sequence […]

2012
PMCID: 3511201
PMID: 22929533
DOI: 10.1186/1479-5876-10-174

[…] nearest neighbor sequence from rdp was recruited into the alignment per input sequence. the alignment was downloaded and trimmed to remove columns whose gap fractions were greater than 50%, using belvu [30]. based on the alignment, a bootstrapped neighbor-joining (nj) tree was subsequently inferred using paupfasta, an in-house wrapper script around the paup* program as described [31], […]

Belvu institution(s)
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
Belvu funding source(s)
Supported by the Wellcome Trust Grant (098051); and the National Human Genome Research Institute Grant (5U54HG00455-04).

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