Software list

Clinical and biological databases:

• Ensembl (https://www.ensembl.org/index.html)
• Ciberer Spanish Variant Server (http://csvs.babelomics.org/)
• Gene Expression Omnibus (https://www.ncbi.nlm.nih.gov/geo/)

Visualization:

• BoxPlotR (http://boxplot.tyerslab.com)
• Heatmapper (http://heatmapper.ca)

Omics-based biomarkers detection and functional profiling:

• Babelomics (http://babelomics.bioinfo.cipf.es/)
• mirPath (http://snf-515788.vm.okeanos.grnet.gr/)
• DAVID (https://david.ncifcrf.gov/)
• STRING (https://string-db.org/cgi/input.pl)
• PANTHER (http://www.pantherdb.org/tools/)
• REVIGO (http://revigo.irb.hr/)

Single-cell analysis:

• ASAP (https://asap.epfl.ch/)

Gene prioritization:

• ENDEAVOUR (https://endeavour.esat.kuleuven.be/)
• ToppGene (https://toppgene.cchmc.org/)

Pathways web tools:

• hiPathia (http://hipathia.babelomics.org/)
• PathAct (http://pathact.babelomics.org/)
• Metabolizer (http://metabolizer.babelomics.org/)

Phylogenetics:

• Aliview
• Blast+
• Clustal-Omega
• FigTree
• Gblocks
• jModeltest
• Megacc
• MrBayes
• RAxML