Example for a phylogenetic PGP tree with clades presented in collapsed mode. See Additional file 1 for all PGP trees and Additional file 4 for a tree summary. Sequences were aligned with MUSCLE, the tree was constructed with PhyML using the WAG matrix (tree “P14”). BphP, Phy, Cph and Fph stands for bacterial, streptophyte, cyanobacterial or fungal phytochrome, respectively. The Greek letters stand for proteobacterial subgroups. If this letter is printed in front of the abbreviation for phytochrome, all members of that clade are in the same subgroup, if printed thereafter, only the majority belongs to that subgroup.