AliView pipeline

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 <>

Publication for AliView

AliView citations

PMCID: 5831051

[…] to estimate divergence times. however, 12.5% of the sequence dataset only had year-specific information; therefore, the date of collection was specified as the mid-point of the corresponding year., aliview version 1.18 [49] was used to concatenate vp72 and cvr into one gene segment (vp72-cvr) for the subsequent analysis. muscle version 3.8.3 was used to align the concatenated sequences […]

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: 5423949

[…] 2014)., for otu-level comparison of hts-detected bacteria with those isolated into culture, the v3–v4 regions were extracted from the full-length 16s rdna sequences from the latter using the program aliview. these spanned from positions 534 to 781 in e. coli, corresponding to the same 247 bp stretch obtained with hts and were clustered with quality-filtered illumina sequences using cd-hit-est […]

PMCID: 5490172

[…] is based on identity of tirs, internal sequences of complete transposable elements and on the breakpoints of deletions., for phylogenetic analysis, the amino acid sequences were aligned with aliview1.18 [39] and the best-fitting ml model (aic, matrix wag + f + i + g) was selected using protest 2.4 server [45]. then, the phylogenetic analysis of transposases was computed using mega6 [46] […]

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) […]

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

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