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

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

August 5, 2014 | Anders Larsson
AliView is a fast and lightweight alignment viewer and editor designed for large phylogenetic datasets. It supports common formats like FASTA, Phylip, Nexus, Clustal, and MSF. The program has an intuitive interface that allows users to inspect, sort, delete, merge, and realign sequences. It is also an easy-to-use editor for both small and large datasets. AliView is open-source under the GNU General Public License version 3.0 and is available on GitHub. It is cross-platform and tested on Linux, Mac OS X, and Windows. It can handle large alignments with low memory usage, loading files 2–14 times faster than other editors and using less than half the memory. AliView can read unlimited size alignment files and uses indexing to manage memory efficiently. It also allows merging overlapping sequences into a consensus sequence, which is useful for next-generation sequencing data. AliView has unique functionality for designing degenerate primers, allowing users to select regions and calculate possible primers based on degenerate positions, self-binding values, and melting temperature. It integrates MUSCLE as the default alignment program and supports external alignment programs. AliView is intended to be a simple, easy-to-use tool for alignment editing, not a complete phylogenetic analysis program. It includes an 'external interface' function to call other programs from within AliView. AliView is compared with other alignment editors in the paper, showing its advantages in speed, memory usage, and functionality.AliView is a fast and lightweight alignment viewer and editor designed for large phylogenetic datasets. It supports common formats like FASTA, Phylip, Nexus, Clustal, and MSF. The program has an intuitive interface that allows users to inspect, sort, delete, merge, and realign sequences. It is also an easy-to-use editor for both small and large datasets. AliView is open-source under the GNU General Public License version 3.0 and is available on GitHub. It is cross-platform and tested on Linux, Mac OS X, and Windows. It can handle large alignments with low memory usage, loading files 2–14 times faster than other editors and using less than half the memory. AliView can read unlimited size alignment files and uses indexing to manage memory efficiently. It also allows merging overlapping sequences into a consensus sequence, which is useful for next-generation sequencing data. AliView has unique functionality for designing degenerate primers, allowing users to select regions and calculate possible primers based on degenerate positions, self-binding values, and melting temperature. It integrates MUSCLE as the default alignment program and supports external alignment programs. AliView is intended to be a simple, easy-to-use tool for alignment editing, not a complete phylogenetic analysis program. It includes an 'external interface' function to call other programs from within AliView. AliView is compared with other alignment editors in the paper, showing its advantages in speed, memory usage, and functionality.
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