NTSYS中文使用说明1.doc

NTSYS-PC使用说明
具体的讨论见
        NTSYS是一个聚类分析的软件，可以用来分析RFLP，RAPD等电泳带型，也可用于微生物群落多样性的相似性分析。下面简单介绍一下其用法：
 1.先建立一个0，1构成的矩阵：在excel中，按如下规则输入数据，A1=1表示有带记为1，B1=9表示RFLP有9个带型， C1=35表示样本数，D1=0表示无带记为0。第二行表示的是样本名称。从第三行开始的A列表示带型名称。见下图：
2. 打开NTSYS-PC程序，点击similarity出现如下界面：

再点击Qualitative data，出现如下界面：

点击input file，打开刚才生成的excel矩阵文件，点击out file起一个文件名（假设叫111），然后点击compute按钮。文件111是一个相似度表。
 3. 继续点击clustering，出现如下界面： 

再点SHAN，出现如下界面：

点击input file，打开文件刚才保存的文件111，点击out file起一个文件名（假设叫222），把In case of ties改为Find，然后点击compute按钮。计算完成！
4. 然后点Graphics, 再点tree plot，出现下面的界面：

点击input file，打开文件222，然后点击compute按钮，就会出现聚类图。
       OK了！
NTSYS-pc software procedures
 Set up Excel spreadsheet
1st row at A1=1 (type of spreadsheet), B1=#rows, C1=#columns, D1=symbol for missing s
2nd row should contain column labels or empty
Matrix should begin on B3 (note row 2 is empty as is column 1)
Save spreadsheet as an xls file
Close excel.
 Making NTSYS matrix
Click on Ntedit
File/import/OLE file
Select excel spreadsheet (matrix should import)
Check matrix to make sure it is in right orientation
Click Col lab button and insert column labels
Do the same for row labels if you want
Save file as what ever you want but should have a spreadsheet.nts extension.
Analysis (note must keep all windows open to proceed to next step)
Open NTSYS-pc program
Click similarity then simqual buttons
Input file click on open space to browse, select spreadsheet.nts file just created
Don’t check by rows
Insert sm in coefficient for similarity matching
Click output file as a text file simqual.nts
Positive code=1.00
Negative code=0.00
Then compute
Print out report file/ notebook/ print/ok.
 Go back to NTSYS-pc screen
Check clustering then SAHN
Input file will be the simqual.nts file above
Output file will be SAHN.NTS
Clustering method=UPMGA
In case of tie=WARN
Maximum # of tied trees=2
Tie tolerance =0.000000000
Beta=0.000000000
Compute.
 Make tree plot
Go to graphics in NTSYS-pc program window
Click tree plot, plot should come in view
File/save file.emf
 To make similarity matrix
Go to NTSYS-pc window
Click general then Dcenter
Input file=simqual.nts
Result matrix=matrix.nts
Compute.
 Ordination
Open NTSYS-pc window
Click ordination
Click eigen
Input matrix= matrix.nts
Dim=3
Output eigenvector.emf
Vector scaling=square lamda
Sample size=0
Degree of freedom=0
 How to make 2D or 3D graph (PCA)
Go to Graphics, then 3D plot, Input file=eigenvector.emf, then don’t check plot by rows, X (1) Y (2) Z (3), Graph matrix file (no), then rotation30.00 30.00, view distance (999.00), then compute.