### Dataset

1. revised 599ntsThis work follows the previous work on http://salsafungiphy.blogspot.com/2013/09/pairwise-distances-from-msa-vs-pairwise.html

This dataset has a total number of 831 sequences.

2. 999nts

This work follows the previous work on http://salsafungiphy.blogspot.com/2013/06/pairwise-distances-from-multiple.html

This dataset has a total number of 1306 sequences.

### Alignment

The clustering was done based on1) SWG, using EDNAFULL scoring matrix, with gap open = -16 and gap extension = -4

2) Multiple sequence alignment, PID.

The Raxml was done based on multiple sequence alignment,

1) revised 599nts, newick file

2) 999nts, newwick file

### Spherical Tree

The information of spherical tree can be found on previous work of http://salsafungiphy.blogspot.com/2012/11/phylogenetic-tree-generation-for.html and http://salsafungiphy.blogspot.com/2012/11/phylogenetic-tree-mega-table.html####
**Dimension Reduction**

**Manxcat SMACOF:**

The pviz file for SWG clustering result with revised 599nts is here, for 999nts is here.

For MSA clustering result with revised 599nts is here, for 999nts is here.

**WDA-SMACOF:**

alpha set to 0.95

The pviz file for SWG clustering result with revised 599nts is here, for 999nts is here.

For MSA clustering result with revised 599nts is here, for 999nts is here.

#### Sum of branch lengths (edge sum)

(note that the difference of edge sum between SWG and MSA should due to the difference of the original distances of the clustering plot)

Manxcat SMACOF | WDA-SMACOF | |||

revised 599nts | 999nts | revised 599nts | 999nts | |

SWG | 19.37 | 19.89 | 16.01 | 12.74 |

MSA | 16.62 | 16.36 | 15.20 | 13.65 |

MSA Result |

SWG Result |

2) 999nts spherical tree

MSA Result |

SWG Result |

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