PWA vs MSA
       • Pairwise sequence alignment (PWA) is much faster 
            and has very high correlation with multiple 
            sequence alignment (MSA).
                                   1.2         MSA        SWG       NW
                                     1
                                  n0.8
                                  o
                                  i
                                  t
                                  a0.6
                                  l
                                  e
                                  r
                                  r
                                  o0.4
                                  C
                                   0.2
                                     0
                                        599nts 454 optimized          999nts
                                   The comparison using Mantel between 
                                   distances generated by three sequence 
                                       alignment methods and RAxML 
          Summarize a million Fungi Sequences
              Spherical Phylogram Visualization
      RAxML result visualized in FigTree.               Spherical Phylogram visualized in PlotViz
                                       MDS methods
        • Sum of branch lengths will be lower if a better 
            dimension reduction method is used.
        • WDA-SMACOF finds global optima
                    599nts with 454 optimized                                        999nts
           30    WDA-SMACOF LMA EM-SMACOF                           25  WDA-SMACOF LMA EM-SMACOF
           25                                                       20
           20
         m                                                        m 15
         u                                                        u
         S 15                                                     S
                                                                   
         e                                                        e
         g                                                        g 10
         d 10                                                     d
         E                                                        E
            5                                                        5
            0                                                        0
                    MSA            SWG            NW                        MSA           SWG            NW
                 Sum of branch lengths of the SP generated in 3D space on 599nts dataset 
                 optimized with 454 sequences and 999nts dataset