I am doing an RNA-seq project, whose aim is to look for lncRNAs of different species. Once I have a set genes that give lncRNAs across different species, I would like to know which genes are orthologous. For proteins, I know that there exists OrthoMCL. However, no idea regarding orthology studies of non-coding genes. Do you know anything about it? There are some tool to use? If not, what do you recommend me to do? Any pipeline?
Thanks in advance.