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Phylo.io specifications

Information


Unique identifier OMICS_11541
Name Phylo.io
Interface Web user interface
Restrictions to use None
Programming languages Javascript
License MIT License
Computer skills Basic
Version 1.0.0
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Christophe Dessimoz

Publication for Phylo.io

Phylo.io citations

 (7)
library_books

Developmental transcriptomics of the brittle star Amphiura filiformis reveals gene regulatory network rewiring in echinoderm larval skeleton evolution

2018
Genome Biol
PMCID: 5831733
PMID: 29490679
DOI: 10.1186/s13059-018-1402-8

[…] d using PRANK []. The resulting alignment was then inspected using sea view and trees were estimated using PhyML v3.1 [] and PhyloBayes MPI 1.6j []. Topological differences are displayed using http://phylo.io []. […]

library_books

Analysis of Piscirickettsia salmonis Metabolism Using Genome Scale Reconstruction, Modeling, and Testing

2017
Front Microbiol
PMCID: 5732189
PMID: 29321769
DOI: 10.3389/fmicb.2017.02462

[…] e G2. Clade membership was confirmed through a phylogenetic tree analysis (Supplementary Figure ) using 16S rDNA sequences. The MAFFT tool () was used for multiple alignment and tree construction and Phylo.io was used for tree visualization (). 16S rDNA sequences of 20 Piscirickettsia strains were downloaded from NCBI including P. salmonis CRG01 while for strain EM-90-like Sanger sequencing was pe […]

library_books

De novo assembly of a transcriptome from the eggs and early embryos of Astropecten aranciacus

2017
PLoS One
PMCID: 5584759
PMID: 28873438
DOI: 10.1371/journal.pone.0184090

[…] ult parameters. The alignment data were converted into a phylogenetic tree by the neighbor-joining algorithm [] with the bootstrap resampling number set at 100. The resulting tree was visualized with Phylo.io 1.0 []. […]

call_split

Mitochondrial haplotypes influence metabolic traits across bovine inter and intra species cybrids

2017
Sci Rep
PMCID: 5482896
PMID: 28646188
DOI: 10.1038/s41598-017-04457-3
call_split See protocol

[…] l gap-free sites were applied to constructing consensus NJ tree with Jukes-Cantor model and 1000 bootstraps by the online MAFFT software, and the consensus tree was depicted using the web application Phylo.io. […]

library_books

A large gene family in fission yeast encodes spore killers that subvert Mendel’s law

2017
eLife
PMCID: 5478263
PMID: 28631610
DOI: 10.7554/eLife.26057.030

[…] with the command line option -m TEST -alrt 1000 -bb 1000 (). The tree was rooted by midpoint rooting using FigTree version 1.4.2 (http://tree.bio.ed.ac.uk/software/figtree/) and was visualized using Phylo.io ().Gene structures of the 57 wtf genes were predicted using the AUGUSTUS web server (version 3.2.3, RRID:SCR_008417) with the parameter settings --genemodel=exactlyone --sample=100 --keep_vit […]

library_books

PIECE 2.0: an update for the plant gene structure comparison and evolution database

2016
Nucleic Acids Res
PMCID: 5210635
PMID: 27742820
DOI: 10.1093/nar/gkw935

[…] w viewer provides users a friendly way to display and analyze intron–exon data within the phylogenetic tree (Figure ) through HTML5 canvas visualization using the open source Javascript library named Phylo.io (). Phylo.io is a web framework to visualize and compare phylogenetic trees side-by-side. The original Plylo.io only displays the trees. Therefore, we modified the source code so that it will […]

Citations

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Phylo.io institution(s)
Department of Computer Science & Department of Genetics, Evolution and Environment, University College London, London, UK; Department of Ecology and Evolution & Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland
Phylo.io funding source(s)
A Summer Research Bursary from the UCL Department of Computer Science; Swiss National Science Foundation grant 150654; UK BBSRC grant BB/M015009/1

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