179x Filetype PPTX File size 0.58 MB Source: dsc.soic.indiana.edu
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
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