**Cluster Matcher**
-------------------
Created 2011 by Emma Hodcroft
Leigh Brown Group, Edinburgh University
=======================================

Input files used:
Data Set 1:
	Newick file: C:\MyDocuments\Clusters\ClusterTutorial\CPoutput\EU1866\EU1866_clusterPicks.nwk
	Annotation file: Will not be used (see '?' below)
Data Set 2:
	Newick file: C:\MyDocuments\Clusters\ClusterTutorial\CPoutput\EU3031\EU3031_clusterPicks.nwk
	Annotation file: C:\MyDocuments\Clusters\ClusterTutorial\TestDataset_3031_epiData.csv

Data set 1 had 1866 sequences and 71 clusters (containing 171 sequences (9.16%))
Data set 2 had 3031 sequences and 228 clusters (containing 640 sequences (21.12%))


*Preview Analysis* (No files written):
60 clusters in data set 1 (84.51%) have more than 1 sequences that match between data sets.
Of these, 40 clusters (56.34%) have at least 1% sequences with a Country value of UNITED KINGDOM in Data Set 1
	Of the 103 sequences in the clusters returned from data set 1:
		- 0 (0.0%) are SPAIN
		- 2 (1.94%) are BELGIUM
		- 0 (0.0%) are GERMANY
		- 0 (0.0%) are FRANCE
		- 97 (94.17%) are UNITED KINGDOM
		- 0 (0.0%) are GREECE
		- 3 (2.91%) are ITALY
		- 1 (0.97%) are CZECH REPUBLIC
		- 0 (0.0%) are DENMARK
		- 0 (0.0%) are CYPRUS
		- 0 (0.0%) have no Country value
	Of the 190 sequences in the matching clusters returned from data set 2:
		- 0 (0.0%) are SPAIN
		- 2 (1.05%) are BELGIUM
		- 0 (0.0%) are GERMANY
		- 0 (0.0%) are FRANCE
		- 178 (93.68%) are UNITED KINGDOM
		- 0 (0.0%) are GREECE
		- 3 (1.58%) are ITALY
		- 1 (0.53%) are CZECH REPUBLIC
		- 0 (0.0%) are DENMARK
		- 6 (3.16%) are CYPRUS
		- 0 (0.0%) have no Country value

*Preview Analysis* (No files written):
16 clusters in data set 1 (22.54%) have more than 2 sequences that match between data sets.
Of these, 12 clusters (16.9%) have at least 1% sequences with a Country value of UNITED KINGDOM in Data Set 1
	Of the 46 sequences in the clusters returned from data set 1:
		- 0 (0.0%) are SPAIN
		- 0 (0.0%) are BELGIUM
		- 0 (0.0%) are GERMANY
		- 0 (0.0%) are FRANCE
		- 43 (93.48%) are UNITED KINGDOM
		- 0 (0.0%) are GREECE
		- 3 (6.52%) are ITALY
		- 0 (0.0%) are CZECH REPUBLIC
		- 0 (0.0%) are DENMARK
		- 0 (0.0%) are CYPRUS
		- 0 (0.0%) have no Country value
	Of the 99 sequences in the matching clusters returned from data set 2:
		- 0 (0.0%) are SPAIN
		- 0 (0.0%) are BELGIUM
		- 0 (0.0%) are GERMANY
		- 0 (0.0%) are FRANCE
		- 92 (92.93%) are UNITED KINGDOM
		- 0 (0.0%) are GREECE
		- 3 (3.03%) are ITALY
		- 0 (0.0%) are CZECH REPUBLIC
		- 0 (0.0%) are DENMARK
		- 4 (4.04%) are CYPRUS
		- 0 (0.0%) have no Country value

*Preview Analysis* (No files written):
60 clusters in data set 1 (84.51%) have more than 1 sequences that match between data sets.
Of these, 41 clusters (57.75%) have at least 1% sequences with a Country value of UNITED KINGDOM in Data Set 2

*Preview Analysis* (No files written):
60 clusters in data set 1 (84.51%) have more than 1 sequences that match between data sets.
Of these, 41 clusters (57.75%) have at least 1% sequences with a Country value of UNITED KINGDOM in Data Set 2

*FigTree Files Written*:
Output Location: C:\MyDocuments\Clusters\ClusterTutorial\CMoutput\2inputFiles
60 clusters in data set 1 (84.51%) have more than 1 sequences that match between data sets.
Of these, 41 clusters (57.75%) have at least 1% sequences with a Country value of UNITED KINGDOM in Data Set 2

**Previously Written Files Were Deleted!**

*FigTree Files Written*:
Output Location: C:\MyDocuments\Clusters\ClusterTutorial\CMoutput\2inputFiles
60 clusters in data set 1 (84.51%) have more than 1 sequences that match between data sets.
Of these, 40 clusters (56.34%) have at least 1% sequences with a Country value of UNITED KINGDOM in both data sets
	Of the 103 sequences in the clusters returned from data set 1:
		- 0 (0.0%) are SPAIN
		- 2 (1.94%) are BELGIUM
		- 0 (0.0%) are GERMANY
		- 0 (0.0%) are FRANCE
		- 97 (94.17%) are UNITED KINGDOM
		- 0 (0.0%) are GREECE
		- 3 (2.91%) are ITALY
		- 1 (0.97%) are CZECH REPUBLIC
		- 0 (0.0%) are DENMARK
		- 0 (0.0%) are CYPRUS
		- 0 (0.0%) have no Country value
	Of the 190 sequences in the matching clusters returned from data set 2:
		- 0 (0.0%) are SPAIN
		- 2 (1.05%) are BELGIUM
		- 0 (0.0%) are GERMANY
		- 0 (0.0%) are FRANCE
		- 178 (93.68%) are UNITED KINGDOM
		- 0 (0.0%) are GREECE
		- 3 (1.58%) are ITALY
		- 1 (0.53%) are CZECH REPUBLIC
		- 0 (0.0%) are DENMARK
		- 6 (3.16%) are CYPRUS
		- 0 (0.0%) have no Country value

**Previously Written Files Were Deleted!**

*FigTree Files Written*:
Output Location: C:\MyDocuments\Clusters\ClusterTutorial\CMoutput\2inputFiles
60 clusters in data set 1 (84.51%) have more than 1 sequences that match between data sets.
Of these, 40 clusters (56.34%) have at least 1% sequences with a Country value of UNITED KINGDOM in both data sets
	Of the 103 sequences in the clusters returned from data set 1:
		- 0 (0.0%) are SPAIN
		- 2 (1.94%) are BELGIUM
		- 0 (0.0%) are GERMANY
		- 0 (0.0%) are FRANCE
		- 97 (94.17%) are UNITED KINGDOM
		- 0 (0.0%) are GREECE
		- 3 (2.91%) are ITALY
		- 1 (0.97%) are CZECH REPUBLIC
		- 0 (0.0%) are DENMARK
		- 0 (0.0%) are CYPRUS
		- 0 (0.0%) have no Country value
	Of the 190 sequences in the matching clusters returned from data set 2:
		- 0 (0.0%) are SPAIN
		- 2 (1.05%) are BELGIUM
		- 0 (0.0%) are GERMANY
		- 0 (0.0%) are FRANCE
		- 178 (93.68%) are UNITED KINGDOM
		- 0 (0.0%) are GREECE
		- 3 (1.58%) are ITALY
		- 1 (0.53%) are CZECH REPUBLIC
		- 0 (0.0%) are DENMARK
		- 6 (3.16%) are CYPRUS
		- 0 (0.0%) have no Country value
