genfamclust

GenFamClust is a homology inference software that takes as input genome synteny (in a specific format) and protein sequences (in fasta format) files and infers homologs and gene families for the input genome(s). What is GenFamClust? GenFamClust (Short for "Gene Family Clustering") is an automated procedure that makes use of syntenic information from species to infer homologous gene families, which are more robust and accurate. These are referred to in literature as syntenic homologs. The program can be used for example in a comparative genomics setting involving multiple species. The algorithm performs better than similarity based tools in terms of accuracy and makes use of regional gene similarity in order to assess the homology relationship between any two genes in the region. The algorithm specifically takes advantage by forming network of blast hits and then using this information to assess the similarity of two genes. Further the algorithm then ass