NeighborNet (NNet) splits graph for 41 taxa. Proteins sequences were aligned with MUSCLE. The initial alignment contained 307 sites including 191 gapped sites that were excluded from the analysis, leaving 116 amino acid sites for log determinant (LogDet) distance estimates with removal of invariant sites using the program LDDist. From this a Neighbor – net splits graph was constructed, which is visualized with Splitstree4. Highlighted are four monophyletic groups: Two of them resemble CpeT-like (phycoerythrin operon protein) proteins (highlighted in green) and two groups harbor members of the Slr1649-like type (highlighted in red). Not shown: The sequences of Synechococcus elongatus PCC 7942 Synpcc7942_0800 and Synechococcus elongatus PCC 6301 Syc0738_d are identical as well as the sequences of Synechococcus elongatus PCC 7942 Synpcc7942_0772 and Synechococcus elongatus PCC 6301 Syc0764_d and the sequences of Prochlorococcus marinus SS120 Pro0342 and Prochlorococcus marinus CCMP1375 orf195.
Bolte et al. BMC Plant Biology 2008 8:56 doi:10.1186/1471-2229-8-56