COG Project Comments

As well as output of program, we link to plot files to be plotted by Plotviz  http://salsahpc.indiana.edu/pviz3/ (latest version http://salsahpc.indiana.edu/pviz3/data/PVIZ3-0.8.11-win64.exe). Note there are mac and Windows version of Plotviz. Currently no Linux version
We also give typical screendumps of 2D projections of 3D mappings. There are 3 heat maps in each case which scatterplot original v mapped distance for
a) Full data sample
b) Distances between points inside 7 clusters (intra)
c) Distances between points in all pairs of 7 clusters (inter) excluding those cases where points inside same cluster
Note on heat map 2 versions of Euclidean histograms are given -- rotated by 90 degrees
There are too many entries to use normal scatterplots; so we use heat maps that can use sophisticated representation of density

Manxcat is one of our two major dimension reduction programs. It can cope with methods like Sammon that have non-unit weight in sum of distance discrepancies. It can also cope with undefined distances

We will adding more explanation

Note Needleman Wunsch, Blast Bitscore and SWG Score give reasonable answers; SWG PID and Blast PID are no good