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AliView specifications


Unique identifier OMICS_05209
Name AliView
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
License GNU General Public License version 2.0
Computer skills Medium
Stability Stable
Maintained Yes


No version available



  • person_outline Anders Larsson

Publication for AliView

AliView citations


NS1 codon usage adaptation to humans in pandemic Zika virus

PMCID: 5942634
PMID: 29768530
DOI: 10.1590/0074-02760170385

[…] of isolation (alignment available from: First, we aligned the coding sequences with MACSE program v0.9 ( and curated it with AliView v1.171 ( Since we previously found evidence for recombination in ZIKV from Africa () and these events could cause potential errors in phylogenetic inferences, we […]


Re visiting the evolution, dispersal and epidemiology of Zika virus in Asia

PMCID: 5940881
PMID: 29739925
DOI: 10.1038/s41426-018-0082-5
call_split See protocol

[…] me dataset included 84 sequences of Asian lineage only. The datasets were aligned with Mafft v.7.266, keeping the reading-frame consistent with amino-acid positions, and were visualized and edited in AliView. All subsequent analyses were performed with a generalized time-reversible nucleotide substitution model with four gamma distributed rate variation categories and a proportion of invariant sit […]


Near full length 16S rRNA gene next generation sequencing revealed Asaia as a common midgut bacterium of wild and domesticated Queensland fruit fly larvae

PMCID: 5935925
PMID: 29729663
DOI: 10.1186/s40168-018-0463-y

[…] Additional filesĀ , , and . Sequences were aligned using the command using the default settings []. The alignment was manually trimmed to remove any remaining primer sequences using the AliView alignment editor []. Sequences that failed to align were manually checked against the NCBI nonredundant nucleotide collection using MegaBLAST. Gaps were removed from the alignment in AliView.N […]


Persistence of the ABCC6 genes and the emergence of the bony skeleton in vertebrates

Sci Rep
PMCID: 5902450
PMID: 29662086
DOI: 10.1038/s41598-018-24370-7

[…] BCC6, ABCC1 and ABCC3 genes (see Supplementary TablesĀ  and ). The sequences of other human ABCC transporters: ABCC 2, 4, 5, 8, 9, 10, 11, 12 and CFTR were also included. Sequences were aligned in the AliView platform using MUSCLE and manually edited to remove sequence gaps and poorly aligned regions. The final edited alignment was used as the input for the construction of phylogenetic tree by: Bay […]


Two new species and one new record of the genus Tylopilus (Boletaceae) from Indian Himalaya with morphological details and phylogenetic estimations

PMCID: 5911683
PMID: 29686503
DOI: 10.3897/mycokeys.33.23703
call_split See protocol

[…] up taxa. Similarly, for the nrITS dataset, two sequences from Gyroporus (KX869874, GQ166901), another genus in Boletales (Gyroporaceae), were used as the outgroup. Phylip file formats were created in AliView () using default settings. Phylogenies were reconstructed using Maximum Likelihood (ML) in RAxML 7.2.6 () in GTRGAMMA substitution model. All parameters in the ML analyses used the default set […]


Massive lateral transfer of genes encoding plant cell wall degrading enzymes to the mycoparasitic fungus Trichoderma from its plant associated hosts

PLoS Genet
PMCID: 5908196
PMID: 29630596
DOI: 10.1371/journal.pgen.1007322

[…] om closely related species, the analysis was repeated using tBlastn. Only published sequences were used. The final set of sequences was realigned using Muscle 3.8.425 [] and integrated in the program Aliview []. Duplicate sequences from the same species were removed. Highly polymorphic regions were removed using the Gblocks [] server with unconstrained parameters. The curated alignments were then […]


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AliView institution(s)
Systematic Biology, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden

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