phylogenetic tree and sequence alignments  (DNASTAR)

Journal: BMC Evolutionary Biology

Article Title: Phylogenetic analysis of CDK and cyclin proteins in premetazoan lineages

doi: 10.1186/1471-2148-14-10

Figure Lengend Snippet: Phylogenetic tree from analysis of CDK family proteins in Homo sapiens , Nematostella vectensis , Thecamonas adhaerens , Amphimedon queenslandica , Monosiga brevicollis , and Salpingoeca rosetta . Maximum likelihood (ML) and Bayesian analyses were conducted using RAxML and PHYLOBAYES 3.3, respectively. Both methods produced trees with nearly identical topologies. The first numbers above branches indicate Bayesian posterior probabilities (only key branches are labeled), and the second numbers above branches indicate ML bootstrap percentages. The scale bar shows the number of substitutions per site. Sequences of Hsa-GSK3alpha, Hsa-MAK, and Hsa-HCDKL1 were used as outgroups. All proteins are labeled with species names followed by accession numbers. Species abbreviations are as follows: Hsa, H. sapiens ; Nve, N. vectensis ; Tad, T. adhaerens ; Aqe, A. queenslandica ; Mbr, M. brevicollis . The alignment used for this analysis is found in Additional file : File S1.

Article Snippet: Multiple sequence alignments and phylogenetic tree files were deposited in Labarchives ( http://dx.doi.org/10.6070/H4RF5S05 ).

Techniques: Produced, Labeling

Journal: BMC Evolutionary Biology

Article Title: Phylogenetic analysis of CDK and cyclin proteins in premetazoan lineages

doi: 10.1186/1471-2148-14-10

Figure Lengend Snippet: Schematic representation of the distribution of different CDK subfamilies in eukaryotic organisms. The results of phylogenetic analyses of CDK family proteins in different organisms are summarized. A black dot indicates the presence of clear homologs of CDK subfamilies or clades (see text for further explanations). Phylogenetic relationships of these organisms are based on recent reports [ , , ] and the results of the Origins of Multicellularity project . Detailed information regarding this figure, including CDK protein accession numbers, is given in Additional file : Table S1.

Article Snippet: Multiple sequence alignments and phylogenetic tree files were deposited in Labarchives ( http://dx.doi.org/10.6070/H4RF5S05 ).

Techniques:

Journal: BMC Evolutionary Biology

Article Title: Phylogenetic analysis of CDK and cyclin proteins in premetazoan lineages

doi: 10.1186/1471-2148-14-10

Figure Lengend Snippet: Tree derived from phylogenetic analysis of cyclin family proteins in H. sapiens , N. vectensis , T. adhaerens , A. queenslandica , M. brevicollis , and S. rosetta . Maximum likelihood (ML) and Bayesian analyses were conducted using RAxML and PHYLOBAYES 3.3, respectively. Both methods produced trees with nearly identical topologies. The first numbers above branches indicate Bayesian posterior probabilities (only key branches are labeled), and the second numbers above branches indicate ML bootstrap percentages. The scale bar shows the number of substitutions per site. Sequences of Hsa-Cables1 and Hsa-Cables2 were used as outgroups. All proteins are labeled with their accession numbers preceded by their species names. Species abbreviations are as follows: Hsa, H. sapiens ; Nve, N. vectensis ; Tad, T. adhaerens ; Aqe, A. queenslandica ; MBr, M. brevicollis. The alignment used for this analysis is found in Additional file : File S3.

Article Snippet: Multiple sequence alignments and phylogenetic tree files were deposited in Labarchives ( http://dx.doi.org/10.6070/H4RF5S05 ).

Techniques: Derivative Assay, Produced, Labeling

Journal: BMC Evolutionary Biology

Article Title: Phylogenetic analysis of CDK and cyclin proteins in premetazoan lineages

doi: 10.1186/1471-2148-14-10

Figure Lengend Snippet: Schematic representation of the distribution of different cyclin subfamilies in eukaryotic organisms. The results of phylogenetic analyses of cyclin family proteins in different organisms are summarized. A black dot indicates the presence of clear homologs of cyclin subfamily members (see text for further explanations). Phylogenetic relationships illustrated for these organisms are derived form a proteome-based phylogeny [ , , ] and the results of the Origins of Multicellularity project . The names of cyclin B-like (cyclins B, A, D, E, J, F, G, I, O, CLB, and CLN); cyclin Y-like (cyclins Y and PCL), and cyclin C-like (cyclins C, H, L, K, T, and Fam58) group members are indicated by different colors. Detailed information regarding this figure, including cyclin protein accession numbers, may be found in Additional file : Table S2.

Article Snippet: Multiple sequence alignments and phylogenetic tree files were deposited in Labarchives ( http://dx.doi.org/10.6070/H4RF5S05 ).

Techniques: Derivative Assay