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Protocols

SeaView specifications

Information


Unique identifier OMICS_08908
Name SeaView
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Computer skills Medium
Version 4.5.4
Stability Stable
Maintained Yes

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Versioning


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Maintainer


  • person_outline Manolo Gouy

Publications for SeaView

SeaView citations

 (907)
library_books

Identification and tissue distribution of chemosensory protein and odorant binding protein genes in Tropidothorax elegans Distant (Hemiptera: Lygaeidae)

2018
Sci Rep
PMCID: 5958050
PMID: 29773848
DOI: 10.1038/s41598-018-26137-6

[…] d OBPs and CSPs from T. elegans and other Hemipteran species were performed using MAFFT (http://mafft.cbrc.jp/alignment/server/clustering.html), and phylogenetic trees were constructed using PhyML in Seaview v.4 using the Jones-Taylor-Thomton (JTT) model with 1000-fold bootstrap replication in neighbor-joining method (NJ). […]

library_books

Hidden MHC genetic diversity in the Iberian ibex (Capra pyrenaica)

2018
BMC Genet
PMCID: 5941765
PMID: 29739323
DOI: 10.1186/s12863-018-0616-9

[…] up to a 96% identity were downloaded and included in the phylogenetic analyses. For comparative purposes all the sequences used in the Amills et al. [] study were included. Sequences were aligned in Seaview v.4.2.11 [] with ClustalW2 [] default settings. The best substitution model for the Bayesian inference (BI) analysis was identified using the Bayesian information criterion (BIC) in jModeltest […]

call_split

Recognition of the genus Thaumatophyllum Schott − formerly Philodendron subg. Meconostigma (Araceae) − based on molecular and morphological evidence

2018
PMCID: 5943393
PMID: 29750071
DOI: 10.3897/phytokeys.98.25044
call_split See protocol

[…] The methodological approach of was followed in order to estimate individual gene trees and a supertree. We have used MAFFT 7 () to individually align the molecular markers and SeaView 4 () to manually adjust them. Bayesian analysis was conducted in MrBayes 3.2.2 (, ) for individual gene trees (Fig. , Suppl. material ) using the GTR + G substitution model. The Markov chain M […]

library_books

Comparative Genomics Reveals the Regulatory Complexity of Bifidobacterial Arabinose and Arabino Oligosaccharide Utilization

2018
Front Microbiol
PMCID: 5928203
PMID: 29740413
DOI: 10.3389/fmicb.2018.00776

[…] nomes was build using the Phylogenetic Tree service included in the PATRIC genomic platform (). Phylogenetic trees for the selected protein families were constructed via the PhyML algorithm () in the Seaview software (), using the default parameters and bootstrap values computed with 100 replicates.The comparative genome analysis and reconstruction of arabinose and AOS utilization pathways were pe […]

call_split

Infant transmitted/founder HIV 1 viruses from peripartum transmission are neutralization resistant to paired maternal plasma

2018
PLoS Pathog
PMCID: 5908066
PMID: 29672607
DOI: 10.1371/journal.ppat.1006944
call_split See protocol

[…] the Los Alamos National Laboratory (LANL) website (http://www.hiv.lanl.gov/content/sequence/GENE_CUTTER/cutter.html) and then refined manually. Full-length envelope sequences were manually edited in Seaview []. The infant T/F env virus sequences were identified by analysing phylogenetic trees and highlighter plots, and infant consensus sequences of the major T/F lineage were generated using the L […]

library_books

Chloroplast variation is incongruent with classification of the Australian bloodwood eucalypts (genus Corymbia, family Myrtaceae)

2018
PLoS One
PMCID: 5905893
PMID: 29668710
DOI: 10.1371/journal.pone.0195034

[…] ned with MAFFT v.7.299b [] and the fast and progressive method FFT-NS-2, suitable for large alignments. One inverted repeat region (IRa) was excluded from the alignment. The alignment was viewed with SeaView v.4.6 [] or Mesquite v.3.10 [] and subsequently processed with GBLOCKS v.0.91b [] using default parameters, which stringently trims alignments allowing no gaps. Hence, the final dataset only i […]

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SeaView institution(s)
CNRS UMR 5558, Biométrie, Génétique et Biologie des Populations, Université Claude Bernard Lyon, Villeurbanne, France

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