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Seqotron specifications

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Unique identifier OMICS_28819
Name Seqotron
Software type Application/Script
Interface Graphical user interface
Restrictions to use None
Input format FASTA,NEXUS,NEWICK,PHYLIP,MEGA,Clustal,NBRF,Stockholm,GDE
Operating system Mac OS
Programming languages C, Objective-C
License GNU General Public License version 3.0
Computer skills Medium
Version 1.0.1
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Mathieu Fourment <>

Publication for Seqotron

Seqotron citations

 (6)
library_books

Comparative genomic analysis of a new tellurite resistant Psychrobacter strain isolated from the Antarctic Peninsula

2018
PMCID: 5822837
PMID: 29479501
DOI: 10.7717/peerj.4402

[…] a protein-coding-guided multiple nucleotide sequence alignment, using translatorx muscle for the multiple sequence alignment (; ). alignments were concatenated using the alignment editor tool seqotron () and the best partition scheme and substitution model was evaluated by partitionfinder2 (). finally, the software mrbayes v3.2 was used for phylogenetic reconstruction (), […]

library_books

The impact of migratory flyways on the spread of avian influenza virus in North America

2017
PMCID: 5445350
PMID: 28545432
DOI: 10.1186/s12862-017-0965-4

[…] downloaded from the influenza virus resource database at ncbi (http://www.ncbi.nlm.nih.gov/genomes/flu/flu.html). for each gene, sequences were aligned using mafft [] and were manually edited using seqotron []. the sampling location within north america was extracted from the sequence name, and each sequence was labelled with a discrete geographic location using either the state classification […]

library_books

Detection of potentially novel paramyxovirus and coronavirus viral RNA in bats and rats in the Mekong Delta region of southern Viet Nam

2017
PMCID: 5811810
PMID: 28418192
DOI: 10.1111/zph.12362

[…] (344 bp; sites 14210–14553 within the genome), a 153‐sequence data set for alphacoronaviruses and a 93‐sequence data set for betacoronaviruses (407 bp; sites 15149–15565 within the genome), using seqotron (fourment & holmes, ). identical sequences and those with greater than 1% ambiguity or missing sequence data were subsequently removed from the alignments. jmodeltest was run, […]

library_books

Comparative Genomics Analysis of a New Exiguobacterium Strain from Salar de Huasco Reveals a Repertoire of Stress Related Genes and Arsenic Resistance

2017
PMCID: 5360010
PMID: 28377753
DOI: 10.3389/fmicb.2017.00456

[…] smpb, and tsf) from the data set (). all nucleotide sequences were translation aligned using mafft () as implemented in geneious v 7.1.9 software (). the alignments were then concatenated using seqotron version 1.0.1 (). a distribution of probable trees using bayesian inference as implemented in mrbayes 3.2.5 was used. two separate runs of 20 million generations were executed (four chains […]

library_books

Comparative analysis estimates the relative frequencies of co divergence and cross species transmission within viral families

2017
PMCID: 5319820
PMID: 28178344
DOI: 10.1371/journal.ppat.1006215

[…] corresponding hosts because they included multiple viruses from a family that can infect the same host., for each virus family nucleotide sequences were first translated to amino acid data using seqotron v.1.0.1 [], aligned with muscle v.3.8 [], and poorly aligned regions then eliminated using trimal [], ensuring that all remaining sequences were at least 100 amino acids in length (). amino […]

library_books

Avian influenza virus exhibits distinct evolutionary dynamics in wild birds and poultry

2015
PMCID: 4481119
PMID: 26111936
DOI: 10.1186/s12862-015-0410-5

[…] hence which could be used to independently assess whether evolutionary rates are elevated in poultry. multiple sequence alignments were generated using mafft version 7 [] and manually edited using seqotron [], with final alignment lengths of 2151 bp, 2271 bp and 2280 bp for pa, pb1 and pb2, respectively. total data set sizes were: h5n1: pa = 479 sequences, pb1 = 411, pb2 = 391; h4: pa = 811, […]


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Seqotron institution(s)
The ithree institute, University of Technology Sydney, Sydney, NSW, Australia; Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Biological Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW, Australia.
Seqotron funding source(s)
Supported by a postdoctoral research fellowship from the University of Sydney and by an NHMRC Australia Fellowship.

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