EvolView protocols

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EvolView specifications

Information


Unique identifier OMICS_04252
Name EvolView
Interface Web user interface
Restrictions to use None
Computer skills Basic
Version 2.0
Stability Stable
Registration required Yes
Maintained Yes

Documentation


Maintainer


  • person_outline Songnian Hu <>

Additional information


https://github.com/evolgeniusteam/EvolviewDocumentation

Publications for EvolView

EvolView in pipelines

 (15)
2018
PMCID: 5902956
PMID: 29661152
DOI: 10.1186/s12866-018-1179-7

[…] []. bootstrap values were calculated using 1000 replicates to generate confidence in the tree topology. the tree generated was viewed and mid point rooted using fig tree (version 1.4.3) [] and evolview v2 []., genomic dna from seven representative s. aureus isolates was extracted using the genelute bacterial genomic dna kit (sigma-aldrich, us) according to the manufacturers instruction. […]

2018
PMCID: 5909903
PMID: 29677198
DOI: 10.1371/journal.pone.0195358

[…] with promals []. the alignment of 161 sequences was subsequently refined with muscle [] and gap-rich columns were removed. a phylogenetic tree was calculated with fasttree [] and visualized with evolview []. the tree was rooted using a thioredoxin-like clade as an outgroup., to determine the effect of mutations on the dynamics of studied proteins, short canonical molecular-dynamics […]

2018
PMCID: 5932348
PMID: 29755425
DOI: 10.3389/fmicb.2018.00764

[…] multiple sequence alignments were performed using clustalw. phylogentic trees were generated using the maximum-likelihood method in phyml version 3.1. phylogenetic trees were annotated using evolview (http://www.evolgenius.info/evolview/#login) (he et al., )., leptospira interrogans strain lai 56601 was obtained from the national institute for the control of pharmaceutical and biological […]

2017
PMCID: 5322909
PMID: 28231283
DOI: 10.1371/journal.pgen.1006546

[…] [] and the alignment manually inspected to remove sequences with incomplete coverage before a phyml maximum likelihood tree was created using the seaview software []. all trees were visualized using evolview []., fixation index (fst) analysis was performed using the r package popgenome []. for all the 1232 core-genome multiple alignments were converted to vcf format using snp-sites [] […]

2017
PMCID: 5340872
PMID: 28270583
DOI: 10.1128/mBio.02014-16

[…] of invariable sites and estimated gamma shape parameter (gtr + i + g). maximum likelihood phylogenetic trees were generated using raxml () using 100 bootstrap replicates. trees were visualized using evolview ()., virus particles were captured using mouse anti-denv mabs 4g2 and 2h2 in carbonate buffer. mabs (see  in the supplemental material) were diluted to a concentration of 20 ng/µl and added […]

EvolView in publications

 (67)
PMCID: 5923176
PMID: 29530862
DOI: 10.1128/AAC.00209-18

[…] significance was evaluated by fisher's exact test. results with ors of >2 or <0.5 and p values of <0.05 (statistical significance) were included., phylograms were visualized using evolview (http://www.evolgenius.info), and histograms and gene synteny were visualized using the statistical software r (v3.3.3; packages ggplot2 and genoplotr) (r foundation for statistical […]

PMCID: 5909903
PMID: 29677198
DOI: 10.1371/journal.pone.0195358

[…] with promals []. the alignment of 161 sequences was subsequently refined with muscle [] and gap-rich columns were removed. a phylogenetic tree was calculated with fasttree [] and visualized with evolview []. the tree was rooted using a thioredoxin-like clade as an outgroup., to determine the effect of mutations on the dynamics of studied proteins, short canonical molecular-dynamics […]

PMCID: 5902956
PMID: 29661152
DOI: 10.1186/s12866-018-1179-7

[…] []. bootstrap values were calculated using 1000 replicates to generate confidence in the tree topology. the tree generated was viewed and mid point rooted using fig tree (version 1.4.3) [] and evolview v2 []., genomic dna from seven representative s. aureus isolates was extracted using the genelute bacterial genomic dna kit (sigma-aldrich, us) according to the manufacturers instruction. […]

PMCID: 5895635
PMID: 29643336
DOI: 10.1038/s41598-018-23985-0

[…] e. phylogenetic relationship of flc homologs (table ) was generated by ml method using gtr + i + g model. the gene structures, protein structures, and all the phylogenetic trees were visualized using evolview software on the website (http://www.evolgenius.info/evolview/)., we used reads per kilobase of exon per million mapped reads (rpkm) to compare the gene expression levels among samples (table  […]

PMCID: 5857598
PMID: 29593678
DOI: 10.3389/fmicb.2018.00428

[…] of nucleotide sequences of one hundred genes present in all strains and in outgroups, with 20 bootstraps. the trees were rooted by closely related, outgroup species. trees were visualized with evolview (zhang et al., ) and itol (letunic and bork, ) web resources. outgroups were selected using the tree obtained from the microbesonline (dehal et al., ) web server as representatives […]

EvolView institution(s)
CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics (BIG), Chinese Academy of Sciences (CAS), Beijing, China; University of Chinese Academy of Sciences, Beijing, China; Institute for Computer Science and Cluster of Excellence on Plant Sciences CEPLAS, Heinrich Heine University, Düsseldorf, Germany; BIG Data Center, Beijing Institute of Genomics (BIG), Chinese Academy of Sciences (CAS), Beijing, China

EvolView review

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Johanna Nelkner

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Web
What an awesome tool!!! I fell in love with it. I could simply upload my newick file and then make the tree look as nice as possible by increasing or decreasing horizotntal or vertical scale, show or hide branch length values, and most important of all: YOU CAN REROOT THE TREE AS YOU LIKE