Table 1.

List of current computational methods for predicting the functional effects of non-synonymous alleles.

Method Name	Description	URL
Align-GVGD [6,7]	Phylogenetic method using phyisco- chemical amino acid properties	http://agvgd.iarc.fr/agvgd_input.php
LRT [9]	Phylogenetic method using estimated rate of evolution	(no server)
LS-SNP [40]	Database of polymorphisms, classified by phylogenetic and structural features combined with machine learning	http://modbase.compbio.ucsf.edu/LS-SNP/
MAPP [5]	Phylogenetic method using patterns of physico-chemical properties of amino acid substitutions	http://mendel.stanford.edu/sidowlab/downloads/MAPP/index.html
MSRV [42.73]	Various phylogenetic methods combined with a custom machine learning algorithm	http://bioinfo.steadybj.com/msrv
nsSNPAnalyzer [74]	Phylogenetic and structural features combined with machine learning	http://snpanalyzer.utmem.edu/
PANTHER [75,76]	Database of polymorphisms, classified by a phylogenetic method using patterns of amino acid substitutions	http://www.pantherdb.org/tools/csnpScoreForm.jsp
PhD-SNP [41]	Phylogenetic method using patterns of amino acid substitutions	http://gpcr2.biocomp.unibo.it/cgi/predictors/PhD-SNP/PhDSNP.cgi
PMut [8]	Phylogenetic and structural features combined with machine learning	http://mmb2.pcb.ub.es:8080/PMut/
PolyPhen-2 [10]	Phylogenetic and structural features combined with machine learning	http://genetics.bwh.harvard.edu/pph2
SIFT [3,4,77]	Phylogenetic method using patterns of amino acid substitutions	http://sift.jcvi.org/
SNAP [11]	Phylogenetic and structural features combined with machine learning	http://cubic.bioc.columbia.edu/services/SNAP/
SNPs3D [20,39,78]	Combination of 2 methods, one phylogenetic and one based on structural features	http://www.snps3d.org/
TopoSNP [38]	Database of polymorphisms, classified by structural features	http://gila.bioengr.uic.edu/snp/toposnp/