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Protocols specifications


Unique identifier OMICS_11541
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




  • person_outline Christophe Dessimoz

Publication for citations


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

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 []. […]


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

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 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 […]


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

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 1.0 []. […]


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

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 […]


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

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 ( and was visualized using ().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 […]


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

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 (). is a web framework to visualize and compare phylogenetic trees side-by-side. The original only displays the trees. Therefore, we modified the source code so that it will […]


Looking to check out a full list of citations? 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 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 reviews

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