Fig. 6
From: Developing a bioinformatics pipeline for comparative protein classification analysis
Phylogenetic analysis derived from Forest Analysis and GO coupled with Pfam terms screening. A: The tree with the highest log likelihood (-38190.90) is shown. The associated taxa clustered together next to the branches are defined by a normalized scale. The bootstrap is highlighted by pink circles (normalized scale from 0 to 1). The internal nodes are represented by rectangular shape in blue and each protein ID is highlighted with dashed lines. The leaf nodes are displayed with a circular shape. ARA = A. thaliana, RA = B. rapa Pekinensis group are the labels to refer to the species. B The tree with the highest log likelihood (-71352.70) is shown. The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. The bootstrap is highlighted by purple circles (normalized scale from 0 to 1). The internal nodes are represented by rectangular shape in green and each protein ID is highlighted with dashed lines. The leaf nodes are displayed with a rectangular shape in red. ARA = A. thaliana, RA = B. rapa Pekinensis group. Four outgroups are also inclided in the tree: Bkt from C. reinhardtii, Pds C. reinhardtii, FNOV0100002 - Brt/brk from H. psycrophilus, P45086A1 - cytochrome P450 from A. thaliana. C The tree with the highest log likelihood (-41791.08) is presented. The bootstrap is highlighted by purple triangles (normalized scale from 0 to 1). The internal nodes are represented by rectangular shape in green and each protein ID is highlighted with dashed lines. The leaf nodes are displayed with a circular shape in red. The four outgroups are included as in the previous analysis. ARA = A. thaliana, RA = B. rapa Pekinensis group are the labels to refer to the species