Jalview protocols

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 IN pipelines

PMCID: 5775359
PMID: 29352135
DOI: 10.1038/s41598-018-19526-4

[…] from both flavivirus and hepacivirus were subjected to multiple amino acid sequence alignment for dpp domain detection and sequence conservation using clustall ows software available through jalview 2.9.074. after final sequence alignment, dpp triamino acid sequence was located using textual search., one-way anova tests followed by a tukey multiple comparison test were used to compare […]

PMCID: 5825034
PMID: 29474388
DOI: 10.1371/journal.pone.0193058

[…] grand island, ny). the transfection reagent (transit) was purchased from mirus bio (mirus bio, madison, wi)., multiple sequence alignments were made by clustal x2 software [12] and formatted in jalview 2.9 [13]. transmembrane helices were predicted using a tmhmm server (http://www.cbs.dtu.dk/services/tmhmm)., t7 promoter sites were incorporated on either side of primers (forward, […]

PMCID: 5836110
PMID: 29343515
DOI: 10.1074/jbc.RA117.001614

[…] protein sequence database (79). sequences of proteins with a minimum query coverage of 60% and a minimum sequence identity of 20% to gtlb were downloaded and used for further analysis in jalview (80). a multiple-sequence alignment of gtlb and its homologs was performed with clustal omega, setting the l. monocytogenes gtlb protein as a reference. the alignment was subsequently used […]

PMCID: 5851622
PMID: 29538447
DOI: 10.1371/journal.pone.0194335

[…] with pam as scoring matrix to align functional motifs of diversified sequences. based on quality of alignment unaligned or packed columns in msa were removed manually using jalview[36] software retaining good quality columns. phylogenetic trees were built based on bayesian inference using mrbayes software version 3.2[37] using mixed amino acid model. markov chain monte […]

PMCID: 5232348
PMID: 28081263
DOI: 10.1371/journal.pone.0170072

[…] primers used in race and rt-pcr were listed in s1 table., an amino acid sequence alignment of the three pameobps with obps from other insects was created using clustalx 2.0 [11] and visualized by jalview 2.4.0 b2 [12]. the three pameobps along with obps from blattella germanica, rhyparobia maderae, holotrichia parallela, zootermopsis nevadensis, coptotermes formosanus, oedaleus asiaticus, […]

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

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