Jalview pipeline

Jalview specifications


Unique identifier OMICS_00885
Name Jalview
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java
License GNU General Public License version 2.0
Computer skills Medium
Stability Stable
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/Jalview



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  • person_outline Geoffrey J. Barton <>

Publications for Jalview

Jalview citations

PMCID: 5784589

[…] v3.965 and visualized using itol—interactive tree of life [35]. sequence alignment of mig1 cds region from 349 to 449 bp of representative fungal species was done by clustalw and visualized using jalview software., the gene and protein sequence of crea of t. cellulolyticus were used for blast searches against the annotated p. funiculosum ncim1228 genome sequence. a single open reading frame […]

PMCID: 5575007

[…] as negatives under one condition may interact under different cell or experimental conditions, as was recently seen with mcas21, 92. sequences were aligned with clustal w 2.093 and displayed in jalview94. e. coli mrna sequence data was retrieved from genolist95 and analysed within a sequence window containing the 5′ utr and the first 80 nts (+1–+80) of the coding sequence. in cases where 5′ […]

PMCID: 5428507

[…] expression and homology data for that genome. the protein sequences were aligned using mafft version 7.12331 with the e-ins-i method. the alignment was visualized and manually curated using jalview 2.8.232. conserved rrxs sites were identified in the alignment. a phylogenetic tree was reconstructed using raxml version 8.1.1633 with the protgammawag model with 100 rapid bootstrap […]

PMCID: 5249191

[…] (aah29254.1), feline (xp_003983558.1), canine (np_001002982.1), cavy (xp_013005826.1), and erinaceine (xp_007533138.1) protein sequences were obtained from genpept. sequences were aligned using jalview 2.9.0b2 and analyzed by clustal x. homology between these cd40 protein sequences was calculated by protein blast to determine percentage identity to swine cd40 sequence., hybridomas, human […]

PMCID: 5223596

[…] sequences that were fragments, duplicates or assigned to a grass other than triticum. the database comprises 634 unique full length cdna sequences and was curated using clustal omega, db-toolkit and jalview (martens et al., 2005; waterhouse et al., 2009; mcwilliam et al., 2013). phylogenetic trees of the complete curated database were created using figtree, and the neighbor joining blosum62 […]

Jalview institution(s)
School of Life Sciences Research, College of Life Sciences, University of Dundee, Dow Street, Dundee, UK

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