How can I further process my DNA fingerprints after analysis with
GelQuest? Can I analyse a binary matrix (01-matrix) with GelQuest?
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By downloading GelQuest you will also receive SequentiX ClusterVis, a tool for the
analysis of binary matrix data. It directly takes over the data from GelQuest.
ClusterVis analyses 01 matrix data using the following methods:
· Imports 01 matrix data, distance matrix data, taxon sets, trees.
· Calculation of distance matrix using various different distance measures:
1. Jaccard (Syn. Jaccard similarity coefficient, Tanimoto similarity, complementary to
Soergel distance = (b+c)/(b+c+d))
2. Russel & Rao
3. Rogers & Tanimoto (Syn. Rogers-Tanimoto)
4. Kulczynski #1 (Syn. Tanimoto)
5. Kulczynski #2
6. Dice (Syn. Dice, Sørensen-Dice, Nei & Li, Sørenson’s coefficient,
Dice similarity
coefficient, Burt coefficient, Pirlot index, Czkanowski, Hodgkin-Richards)
7. Pearson Phi coefficient (Syn. Phi coefficient, Pearson Phi coefficient, Pearson)
8. - bc -
9. Baroni-Urbani/Buser (Syn. Baroni-Urbani, Baroni-Urbani/Buser)
10. Braun-Blanquet
11. Michael
12. Sokal and Sneath #1 (Syn. Sokal and Sneath 1., Anderberg, sometimes anti-Dice)
13. Sokal and Sneath #2 (Syn. SokalSneath 2, un4)
14. Sokal and Sneath #3 (Syn. SokalSneath 3, un5, Gower2 [e.g. in ‘Stata’ software])
15. Simple Matching (Syn. Simple Matching, Apostol, Sokal & Michener, Kendall, Zubin,
Mean Hamming, Sokal's measure, Mean Manhattan, Manhattan distance, city block
metric, taxi-cab, Mean Hamming distance, Binary Squared Euclidian mean distance,
Averaged squared distance)
16. Ochiaï #2 (Syn. Ochiaï #2)
17. Yule Sigma (Syn. Yule Sigma)
18. Hamann (Syn. Hamann, Hamann binary similarity coefficient)
19. Lance & Williams distance (Syn. Lance & Williams distance, Bray-Curtis nonmetric
coefficient)
20. Mean Euclidian distance
21. Weighted Euclidian Distance
22. U cost
23. R cost
24. T combined cost
25. Dispersion (Syn. Dispersion, binary dispersion coefficient)
26. Mountford
· Calculation of dendrograms using Neighbor-Joining and UPGMA clustering methods
· Resampling tests: bootstrapping, delete-halfjackknifing and jackknifing
· Principal coordinates analysis
· Visualisation of cladograms as phylogram, unrootet trees (radial layout, circular tree),
cladogram, elliptogramm, curvogram and rectangular cladogram
· Export of all data (taxon list, binary matrix, distance matrix, trees, etc.).