PhyTree Visualized on 100k+197+420 (score distance)

Description

Environment: Polar Grid (Quarry); 100 nodes (800 cores)
Runtime: Twister
Algorithm: DA-SMACOF

Aligner: SmithWaterman
ScoringMatrix: EDNAFULL
GapOpen: -16
GapExt: -4
DistanceType: (1-Normalized Score)
With Reverse Compliment: Yes
Method: All Varied

Total Time: 4006.004 Seconds.

Dataset

1) 100k selected from 440k; (id:617~100196)
2) 123 consensus sequence; (id: 420~542)
3) 74 sequences from Gen Bank; (id: 543~616)
4) 420 sequences as new centers; (id: 0~419)

MDS Configuration

[1. Num map tasks ]
[2. Input Folder]
[3. Input File Prefix]
[4. IDs File ]
[5. Label Data File ]
[6. Output File ]
[7. Threshold value ]
[8. The Weighted Flag ]
[9. The Target Dimension ]
[10. Cooling parameter (alpha) ]
[11. Input Data Size]
[1. Num map tasks ]: 800
[2. Input Folder]: /N/dc/scratch/yangruan/matrix/haixu/800/
[3. Input File Prefix]: 100617_800p_
[4. IDs File ]: /N/dc/scratch/yangruan/matrix/haixu/100k+197+420_800p.idx
[5. Label Data File ]: NoLabel
[6. Output File ]: /N/dc/scratch/yangruan/fasta/haixu/440k/100k_197_420/100617_score_dasmacof.txt
[7. Threshold value ]: 1.0E-6
[8. The Weighted Flag ]: 0
[9. The Target Dimension ]: 3
[10. Cooling parameter (alpha) ]: 0.95
[11. Input Data Size]: 100617

Tree Configuration

New sequences from Gen Bank: Hexagon
OK sequence in Haixu Consensus: Triangle
Not OK sequence in Haixu Consensus: Rectangle
Root: Sphere

Color Scheme:  Phylogenetic tree generated here

Final Result

1. Plot File in PVIZ format

Screen Shot