1. Go to https://bioinformatics.psb.ugent.be/plaza/. Here you
can find all of the species supported by PLAZA. Select the
appropriate PLAZA instance (in this case “Dicots PLAZA
4.0”).
2. Search for “AT3G24650” under Dicots PLAZA (choose
“Search” in the menu bar).
3. Scroll down to the Toolbox. Click on the option to view the
phylogenetic tree of the homologous gene family. This will
display a phylogenetic tree with the information of all plant
species stored in PLAZA.
4. Since the previous tree can be difficult to navigate due to the
overwhelming amount of information, PLAZA V4 has a function to create a custom tree using the Interactive Phylogenetics
Module in its toolbox. Figure 2 is one such tree, made by
0.89
0.95
0.97
0.10
54
0.63
98
0.86
98
0.42
0.39
0.51
0.24
0.64
0.14
0.14
0.11
0.06
0.26
1.27
ATIG13260
AT3G25730
AT1G51120
AT1G25560
AT1G68840
AT2G46870
AT4G32010
AT2G30470
AT4G21550
AT1G28300
AT3G26790
AT3G24650
0.09
0.06
0.12
0.95
94
100
92
67
44
84
Fig. 2 Custom PLAZA tree showing ABI3 paralogs. Note that most of these aren’t
well-supported (bootstrap value of 54 for first the node on the left)
32
G. Alex Mason et al.