Fig. 6
From: String kernels for protein sequence comparisons: improved fold recognition
Inferred RNA polymerase phylogeny. Five different phylogenetic trees were constructed for a group of 10 RNA polymerases, using five different distance measures between their sequences: (a) the original distances proposed by Thorne and Kishino [38], (b) distances derived from a Multiple Sequence Alignment of the 10 sequences computed with Clustal Omega [60], (c) the BIT distances from FASTA SSEARCH tools, and the distances computed with SeqKernel with two different settings, namely (β,k max )=(0.2,10) (d) and (β,k max )=(0.0001,2) (e). Abbreviations for species names are provided in Table 4. Branches corresponding to eukaryotic sequences are colored red, those for archaebacterial sequences are shown in blue, and the eubacterial and chloroplast sequences are highlighted in orange and green, respectively