AliView protocols

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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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Maintainer


  • person_outline Anders Larsson <>

Publication for AliView

AliView in pipelines

 (15)
2018
PMCID: 5850367
PMID: 29389912
DOI: 10.3390/v10020060

[…] and the stanford drug resistance database quality assessment tool. sequences were aligned using hivalign (options: mafft, codon-alignment) [] and visualized using aliview []. phylogenetic inference was performed by maximum likelihood using phyml under a general time reversible model of nucleotide substitution [] on nucleic acid alignments trimmed to protease […]

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

[…] 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 […]

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, […]

2017
PMCID: 5381553
PMID: 28201585
DOI: 10.1093/gbe/evx022

[…] guidance v2.0 () anchored by codons using mafft v7.0 () with 100 pseudoreplicate guide trees. concatenation of the multiple alignment was done by fasconcat (). manual curation was then performed in aliview (), 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 […]

2017
PMCID: 5408087
PMID: 28419285
DOI: 10.1093/gbe/evx067

[…] and one outgroup (katsuwonus pelamis), retrieved from genbank (). all sequences were jointly aligned using the “- -auto” option in mafft v7.158b () and the alignment was visually checked using aliview v1.16 (). a maximum likelihood tree search with ten individual runs was performed under the gtrcat substitution model using raxml v8.0.26 (), and node support was assessed with up to 1,000 […]


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AliView in publications

 (72)
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, […]

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 […]

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 […]

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: […]

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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