I could not access the page for Plant genome duplication database, and couldn't find any other database and related tools to analyze my sequences for gene duplication...
Maybe try duplicated genes database (DGD), ohnologs v2. I'm not sure if you could replace it with a method, like SCORPiO, for tree phylogeny. Hope it helps.
Thank you so much for the suggestions, unfortunately DGD is only working with the 9 available species in it's database and both databases are not for plant genome..
I'm currently working on common bean genome, and all references I came across suggest the plant genome duplication database (PGDD), However I can't even reach the webpage (http://chibba.agtec.uga.edu/duplication/) as it refuse to connect.. and I couldn't find any alternative so for...
I did use the tools in Phytozome 12 and 13 for the genome wide screening for the gene families I'm working with, the next step is to analyze the tandem gene duplication...
Yep, the address (http://chibba.agtec.uga.edu/duplication/) you provided for PGDD did not work (see attachment). I have requested an answer from the authors [1].
Phytozome doesn't have tools to analyze the tandem duplication, all literatures I came across uses phytozome for analysis of distribution of certain genes/proteins in the genome, then the the tandem and segmental duplication is analyzed by the PGDD..