I'm working on some bioinformatic analysis of a non-model woody plant within the family with least information. So, I'm looking for a closest species to my plant. Any suggestion would be highly appreciated. Also, It will be great if I have know about the divergence time (? million year) between two species. Is there any documents or website to address this issue? Thanks
If you know the species name, you can search TreeBase to find previously published phylogenetic trees which will point you towards close relatives to your species. Depending on how obscure your taxon is, though, you might not find much.
Maybe you could get some information from the Angiosperm Phylogeny Group: http://www.mobot.org/MOBOT/research/APweb/
They even have a tree where model organisms are highlighted: http://www.mobot.org/MOBOT/research/APweb/trees/modeltreemap.html
You can try http://timetree.org/ to get the divergence time if you already have the names of the taxa.