Orthograph: a versatile tool for mapping coding nucleotide sequences to clusters of orthologous genes

BMC Bioinformatics

Table 1 Results from the tests that compare Orthograph performance to HaMStR [3]

Software	Test	Genes	Species	OGS	Found	TP	FP	FN	Sens.	Acc.
Orthograph	Single-copy	4625	A. mellifera	15,314	4582	4577	5	48	0.990	0.996
Orthograph	Single-copy	4625	H. saltator	18,564	4590	4587	3	38	0.992	0.997
HaMStR	Single-copy	4625	A. mellifera	15,314	4589	4588	3	39	0.992	0.997
HaMStR	Single-copy	4625	H. saltator	18,564	4573	4571	2	54	0.988	0.996
Orthograph	Isoforms	8	C. floridanus	17,064	7	7	0	1	0.875	0.999
HaMStR	Isoforms	8	C. floridanus	17,064	7	7	0	1	0.875	0.999
Orthograph	Inparalogs	647	A. cephalotes	18,093	583	583	0	6	0.901	0.996

Sensitivity is defined as the ratio of true positives (TP) to TP plus false negatives (FN). Accuracy is defined as the ratio of TP plus true negatives (TN) to the total number of genes in the official gene set (OGS). FP, false positives. Note that the results are meant to demonstrate equality in performance despite algorithmic differences

ISSN: 1471-2105