Table 2 Currently available ortholog identification tools
From: geneHummus: an R package to define gene families and their expression in legumes and beyond
Tool | Purpose and Features | Platform |
|---|---|---|
HomoloGene | ● Constructs orthologous groups from the complete gene sets of 21eukaryotic species ● Includes only species with a complete genome or at least 10,000 UniGene entries | ● Web interface |
MultiMSOAR | ● Identifies ortholog groups among multiple genomes ● Genome should be closely related | ● Linux |
OrthoMCL | ● Groups proteins into ortholog groups based on their sequence similarity | ● Galaxy server ● Linux |
GeneSeqToFamily | ● Finds orthologous genes and their corresponding gene families using the Ensembl Compara GeneTrees pipeline | ● Galaxy server |
OrthoFinder | ● Identifies orthologous protein sequence families | ● Linux |
Ensembl Plants | ● Utilizes reference genome sequences as a framework to integrate variant, functional, expression, marker, and comparative data for a number of plant species ● Ensembl plants does not include most legumes | ● Web interface ● API |
geneHummus | ● Uses the Refseq Database, which is dynamically growing and manually curated ● Sequence data is streamed within cloud or local infrastructure so it doesn’t require downloading of genomic or protein sequences | ● R ● Linux |