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


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  • person_outline Anders Larsson <>

AliView article

AliView citations

PMCID: 5574811

[…] model (lset nst = 1 coding = noabsencesites) and discarding the first 25% generations as burn‐in., sequences of the its region were aligned by mafft 7 (katoh & standley, 2013) and edited using aliview (larsson, 2014). in addition, we included in the final matrix previously published its sequences of: (1) 11 directly sequenced accessions of other andean senecio (pelser et al., 2007) and (2) […]

PMCID: 5381553

[…] v7.0 (katoh and standley 2013) with 100 pseudoreplicate guide trees. concatenation of the multiple alignment was done by fasconcat (kück and meusemann 2010). manual curation was then performed in aliview (larsson 2014), and whenever local regions were misaligned we used the software “realign selected block” option and updated the information about each gene start and end. amount of variable […]

PMCID: 5292420

[…] et al., 2015). a concatenated set of three genes from the strains listed in table 1 and supplementary table s1, was used to create an alignment using muscle v3.8.425 (edgar, 2004) tool integrated in aliview (larsson, 2014). the conserved concatenated alignment based on nucleotides containing 2604 characters was subjected to bayesian analysis using program mrbayes v3.2.5 (huelsenbeck […]

PMCID: 4936521

[…] with their respective homologues using the programme mafft v7.123b (katoh and standley 2013). the multiple sequence alignments were individually analysed and manually edited with the program aliview (larsson 2014). the phylogenetic analyses were conducted using beast2 (bouckaert et al. 2014) with different datasets consisting of the nuclear 18s rrna gene, and the mitochondrial genes 16s […]

PMCID: 5635594

[…] were generated for hepacivirus and pegivirus complete coding sequences. alignments were constructed using the mafft program (katoh and standley 2013) followed by substantial manual editing using aliview (larsson 2014). we then used the bmge program (criscuolo and gribaldo 2010) to trim the multiple amino acids alignments prior to phylogenetic analysis, in order to remove poorly aligned […]

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

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