Belvu statistics

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Citations per year

Number of citations per year for the bioinformatics software tool Belvu
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Tool usage distribution map

This map represents all the scientific publications referring to Belvu per scientific context
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Protocols

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


No version available

Maintainer


  • person_outline Gemma Barson

Additional information


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

Publications for Belvu

Belvu citations

 (19)
library_books

Comparative Transcriptomics Among Four White Pine Species

2018
PMCID: 5940140
PMID: 29559535
DOI: 10.1534/g3.118.200257

[…] Functional annotations were merged from EnTAP to further characterize the results.Multiple sequence alignments of each conserved gene family were prepared with Muscle (). Alignments were evaluated in Belvu by conservation scores and those with excessive gaps and missing data were filtered (). Pairwise alignments across all four species were evaluated with codeml (PAML, v.4.6) (). The tree file was […]

library_books

A non canonical mismatch repair pathway in prokaryotes

2017
Nat Commun
PMCID: 5290159
PMID: 28128207
DOI: 10.1038/ncomms14246

[…] e-value (removed >0.0001), bit score >50, and length (only those >75% length were kept), and further aligned by MAFFT [ http://mafft.cbrc.jp/alignment/software/]. The alignments were visualized with Belvu [ http://sonnhammer.sbc.su.se/Belvu.html] to check for quality. We removed the redundancy of the alignment discarding sequences with more than 63% of sequence identity. We next generated Markov […]

call_split

The role of ADP ribosylation in regulating DNA interstrand crosslink repair

2016
PMCID: 5087659
PMID: 27587838
DOI: 10.1242/jcs.193375
call_split See protocol

[…] ns were performed with PsiPred ().Protein amino acid sequences were obtained from UniProt or dictyBase (; ). Alignments of protein sequences were performed using MUSCLE or T-Coffee, and visualised in Belvu (; ; ). DNA sequences were aligned using the MultAlin interface (). […]

call_split

Comparative analysis of plant immune receptor architectures uncovers host proteins likely targeted by pathogens

2016
BMC Biol
PMCID: 4759884
PMID: 26891798
DOI: 10.1186/s12915-016-0228-7
call_split See protocol

[…] am (HMMER2.0) []. 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 [].The evolution of TIR_2 domains was inferred with MEGA5 [] using the maximum likelihood method bas […]

library_books

What Makes a Bacterial Species Pathogenic?:Comparative Genomic Analysis of the Genus Leptospira

2016
PLoS Negl Trop Dis
PMCID: 4758666
PMID: 26890609
DOI: 10.1371/journal.pntd.0004403

[…] alignment to the bacterial 16S rRNA reference alignment using Ribosomal Database Project release 10 (RDP-X) []. The aligned FASTA sequences were downloaded and trimmed to remove gapped columns using Belvu (v2.31) []. Based on the alignment, a bootstrapped Maximum-likelihood tree was subsequently inferred using phylipFasta, an in-house wrapper script [] for the Phylip program [, ].SecY trees were […]

call_split

Domain atrophy creates rare cases of functional partial protein domains

2015
Genome Biol
PMCID: 4432964
PMID: 25924720
DOI: 10.1186/s13059-015-0655-8
call_split See protocol

[…] equences and homologous sequences from a JackHMMER search []. A non-redundant set of sequences of 90% identity or less was aligned with Mafft [] with default settings. Alignments were visualised with Belvu [] and phylogenetic trees constructed using the neighbour-joining method present in Belvu using default parameters. […]


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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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