To test the relationship between MSI and phylogenetic relatedness, multiple phylogenetic similarity matrices were constructed for all of the taxa examined, using recently published phylogenetic hypotheses [33] [43].
We performed multiple phylogenetic analyses of these sequences with up-to-date phylogenetic methods.
The identification within several kinesin families of paralogs shared by multiple eukaryotic supergroups suggests that the use of family name alone does not accurately reflect the evolutionary (or functional) complexity of the kinesin motor families.
Multiple alignments and phylogenetic analysis strongly suggested that RpPLYZ was a new member of the phage-type lysozyme family.
Multiple alignments and phylogenetic relationship strongly suggested that VpCLYZ-1 and VpCLYZ-2 belonged to the c-type lysozyme family.
Multiple alignment and phylogenetic analysis were performed using MEGA6 [ 19].
The resulting p values were corrected for multiple comparisons at each phylogenetic level using the Benjamini-Hochberg correction (FDR).
For phylogenetic analysis, multiple protein sequence alignments were built using ClustalW [37].
Multiple sequence alignments and phylogenetic reconstruction were performed as previously described [12].
Multiple-sequence alignments and phylogenetic trees were generated by using the CLUSTALW software (Figure S3).
