Phylo.io

[…] 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 []. […]

[…] 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 […]

[…] 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 []. […]

[…] 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. […]

[…] 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 […]

[…] 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 […]