AliView: a fast and lightweight alignment viewer and editor for large datasets

By Anders Larsson. Bioinform., 2014

3,282 citations recorded by the source corpus.

Summary: AliView is an alignment viewer and editor designed to meet the requirements of next-generation sequencing era phylogenetic datasets. AliView handles alignments of unlimited size in the formats most commonly used, i.e. FASTA, Phylip, Nexus, Clustal and MSF. The intuitive graphical interface makes it easy to inspect, sort, delete, merge and realign sequences as part of the manual filtering process of large datasets. AliView also works as an easy-to-use alignment editor for small as well as large datasets. Availability and implementation: AliView is released as open-source software under the GNU General Public License, version 3.0 (GPLv3), and is available at GitHub (www.github.com/AliView). The program is cross-platform and extensively tested on Linux, Mac OS X and Windows systems. Downloads and help are available at http://ormbunkar.se/aliview Contact: anders.larsson@ebc.uu.se Supplementary information: Supplementary data are available at Bioinformatics online.

Subfields: Information Systems and Management, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/7dc089d3001586244d8d3700ad1ae25bc24deaa0

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Citations in the corpus

Investigating species boundaries in Colletotrichum (2021, methodology): “The alignments were manually improved using BioEdit v. 7.0.5.2 (Hall 1999) and AliView v. 1.26 (Larsson 2014).”
Microfungi associated with Clematis (Ranunculaceae) with an integrated approach to delimiting species boundaries (2020, methodology): “2019) (http:// mafft .cbrc.jp/align ment/serve r), with minimal adjustment of the ambiguous nucleotides by visual examination and manually corrected in AliView program (Larsson 2014).”
MSAViewer: interactive JavaScript visualization of multiple sequence alignments (2016, neutral): “Many tools are available to view and analyze MSAs, including standalone applications (Larsson, 2014; Waterhouse et al. , 2009) and web app-lets (Waterhouse et al. , 2009).”
Applied aspects of methods to infer phylogenetic relationships amongst fungi (2020, methodology): “1) (Hall 1999) or AliView (Larsson 2014) to assure the sequence quality.”
In honor of John Bissett: authoritative guidelines on molecular identification of Trichoderma (2021, methodology): “• Insert the sequences in Aliview and use “Realign everything” option in “Align” menu.”