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Protocols

AliView specifications

Information


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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No version available

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Maintainer


  • person_outline Anders Larsson

Publication for AliView

AliView citations

 (77)
library_books

NS1 codon usage adaptation to humans in pandemic Zika virus

2018
PMCID: 5942634
PMID: 29768530
DOI: 10.1590/0074-02760170385

[…] of isolation (alignment available from: https://github.com/caiofreire/cub). first, we aligned the coding sequences with macse program v0.9 (https://bioweb.supagro.inra.fr/macse/) and curated it with aliview v1.171 (http://ormbunkar.se/aliview/). since we previously found evidence for recombination in zikv from africa () and these events could cause potential errors in phylogenetic inferences, […]

call_split

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

2018
PMCID: 5940881
PMID: 29739925
DOI: 10.1038/s41426-018-0082-5
call_split See protocol

[…] 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 […]

library_books

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

2018
Microbiome
PMCID: 5935925
PMID: 29729663
DOI: 10.1186/s40168-018-0463-y

[…] additional files , , and . sequences were aligned using the align.seqs.py 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 […]

library_books

A11 The 1988 Elista outbreak and the epidemiology of HIV subtype G in Russia

2018
Virus Evol
PMCID: 5905505
DOI: 10.1093/ve/vey010.010

[…] 122 sequences of russian origin from the los alamos national laboratory (lanl) hiv database (lanl.hiv.gov). sequences were aligned with clustal omega, and the alignment was then manually edited in aliview. a maximum likelihood tree was reconstructed using raxml. in the resulting phylogeny, the 120 russian lanl sequences and the three crie sequences from the elista outbreak fall into a clade […]

library_books

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

2018
Sci Rep
PMCID: 5902450
PMID: 29662086
DOI: 10.1038/s41598-018-24370-7

[…] abcc1 and abcc3 genes (see supplementary tables  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: […]

library_books

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

2018
PMCID: 5911683
PMID: 29686503
DOI: 10.3897/mycokeys.33.23703

[…] 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 […]


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

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