Compute percentage of similar segments used when comparing a variety pair

[ddaspit]

Here is the request from Wyn Owen:

"Say I specified 20 similar segments, could Cog count the number of these that were used in a particular comparison, eg 15 out of the 20 were used when comparing Variety 2 with Variety 5? The results could be put into a matrix in percentage form. This would give a quick view of differences between pairs that might point to varieties that need further investigation."