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AltAVist specifications


Unique identifier OMICS_24725
Name AltAVist
Alternative name Alternative Alignment Visualization Tool
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes


No version available


  • person_outline Burkhard Morgenstern

Publication for Alternative Alignment Visualization Tool

AltAVist citations


IVisTMSA: Interactive Visual Tools for Multiple Sequence Alignments

Evol Bioinform Online
PMCID: 4362671
PMID: 25861209
DOI: 10.4137/EBO.S18980

[…] ment by column are also the unique features of MSA-pad. Some of the alignment editors such as HOMED and MALIGNED are no longer maintained by their authors. Several tools such as Suite MSA, SinicView, AltAVist, and BALiBASE c program are available to compute SPS and CS but they cannot process more than 1,000 sequences. Results showed that the MSA comparator was 5,200% efficient as compared to BALiB […]


Hepatitis C Virus Phylogenetic Clustering Is Associated with the Social Injecting Network in a Cohort of People Who Inject Drugs

PLoS One
PMCID: 3482197
PMID: 23110068
DOI: 10.1371/journal.pone.0047335
call_split See protocol

[…] HCV core sequences were aligned using Clustal W through MEGA version 4.0 and MUSCLE –. The alignments were compared using the AltAVisT web tool and edited by hand where appropriate . An initial evolutionary history was inferred using the neighbour-joining method, with sequence distances calculated using the maximum composite […]


Embryogenic potential and expression of embryogenesis related genes in conifers are affected by treatment with a histone deacetylase inhibitor

PMCID: 3162143
PMID: 21541665
DOI: 10.1007/s00425-011-1418-8
call_split See protocol

[…] nments of 28 HAP3 genes were initially compiled using the MUSCLE and ClustalX algorithms in the program Geneious 5.0 (Drummond et al. ). Both alignments were then compared for discrepancies using the AltaVist alternative alignment visualization tool v. 1.0 (Morgenstern et al. ) before manual refinement and back-translation using Geneious. The nucleotide alignment was used for phylogenetic analyses […]


Odorant Binding Proteins of the Red Imported Fire Ant, Solenopsis invicta: An Example of the Problems Facing the Analysis of Widely Divergent Proteins

PLoS One
PMCID: 3031547
PMID: 21305009
DOI: 10.1371/journal.pone.0016289
call_split See protocol

[…] were compared using a range of ad hoc heuristic criteria. First, we visually compared alignments for congruence in their ability to align sections of the alignments (especially the inner core) using AltAVisT and the overall sequence identity calculated from each alignment. We then tested for sequence saturation using both the Steel (for amino acids; ) and the Xia (for nucleotides ) methods usin […]


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AltAVist institution(s)
International Graduate School in Bioinformatics and Genome Research, Bielefeld, Germany; Faculty of Technology, Research Group in Practical Computer Science, Bielefeld, Germany; Department of Mathematics, University of Bielefeld, Bielefeld, Germany

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