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Table 1 Comparison with other web servers features

From: GenIO: a phenotype-genotype analysis web server for clinical genomics of rare diseases

Feature \ Web servers PhenIX eXtasy OMIM Explorer Phen-Gen wAnnovar GenIO
Year of last update 2014 2013 2016 2013 2015 2017
Simple Input interface Yes Yes No Yes Yes Yes
Acceptance of VCF files Yes Yes Yes Yes Yes Yes
Phenotype (HPO terms) Yes Yes Yes IDs only Yes Yes
Phenotype (OMIM terms) No No Yes No Yes Yes
List of genes of interest to analyze No No Yes No No Yes
Customizable Rareness of the condition Yes No Yes Yes Yes Yes
Fast responsive interface Yes Yes No Yes Yes Yes
No need of extra files to run Yes Yes Yes No Yes Yes
Trio datasets No No No Yes No No
Freeform text input No No Yes No No No
Email notification No Yes No Yes Yes Yes
Dominant and Recessive in single run Yes No Yes No Yes Yes
Can be used by a medical practitioner Yes No Yes No Yes Yes
Output interface with results Yes No Yes No Yes Yes
Simple Output interface Yes No Yes Yes
ACMG-AMP Classification No No No No No Yes
M-CAP Classification No No No No No Yes
ClinVar Classification Top 20 only No No No Yes Yes
ACMG Secondary findings No No No No No Yes
Full VCF annotation No No No No Yes Yes
Handful set of candidate variants Yes No Yes Yes Yes Yes
Session saving No Yes Yes Yes Yes Yes
Phenotype suggestion No No Yes No No No
Secure server (https) No No No No No Yes
Multi-nucleotide variants Yes No Yes Yes Yes Yes