NTsys

NTsys is a program to calculate various comparisions between taxonomic data, e.g. microsatellite DNA analysis (MSDA) data.

Simple use of the program
  1. Set up the input data file:
    For MSDA data, convert the intensities to 0=missing and 1=present for each band.
    Delete all irrelevant information in the file, but keep the first row with band lengths and one column with sample lables (or better one with species and the second with sample lables, which then are merged).
    Save the file as a text file (csv or txt). Use space as the field limiter.
    Each field must be separated by at least one blank space (not tab or comma).
    With the note pad, add a initial title line, starting with " as the first character.
    The second line should contain the type and size of the file with four numbers:
    1: Type: 1=rectangular matrix
    2: #rows
    3: #columns
    4: 0=no missing data present or 1=missing data present, followed by the number for missing data, e.g. 99 or 999
    2 and 3 can be followed by a letter L, B or E, indicating that a lable is added as a separate field, before, or after the entry. Easiest is to use B for rows and L for columns. See an example below.
    When going from Mac to PC, you have to insert a line break before each line

  2. Start ntsys

  3. Go to Dis/similarity tab.
    Select Qulitative data
    Find the input file (you need to show all files, instead of onlh NTS files)
    Check by rows
    Select a coefficient. J is Jacard index; M is Manhattan
    Set the name of an output file
    Positive and negative codes can be kept
    Click on Compute to start the program
    This gives you a Jacard similarity matrix
    Close the report listing window.

    alternatively: use Internal data (sim int); Manhattan; by row; compute

  4. Go to Transformation tab.
    Select Dcenter
    Use the results from the previous calculation as the input file
    Select an output file
    Keep Square distances checked.
    Click on Compute to start the program
    This is needed before ordination
    Close the report listing window.

  5. Go to Ordination tab.
    Select Eigen
    Use the results from the previous calculation as the input file
    Select an output file
    All the default values are OK, but you could use more dimensions or check Show details.
    Click on Compute to start the program
    This performs the PCA.
    Early in the output, you can see the eigenvalues and how much of the variation that is explained by the different components.

    You get the 2D-plot by clicking in the NTSYSpc window, lower left corner on the first button.
    You get the 3D-plot by clicking in the NTSYSpc window, lower left corner on the second button.
    Click on Options - Plot Options - Points - Labels - Labels to see the labels

  6. Cluster
    SAHN
    läst Jaccard file
    out UPGMA

  7. Mega-X
    gör träd



Example of input file

"Rubus data exported 20/1-19
1 4B 5L 1 99
144 146 148 150 152 #This is the column lables
tv-tv96 0 1 1 1 1 #First column is row lables, first species than collect id
tv-tv97 0 1 1 1 1
tv-tv98 0 1 1 1 1
tv-tv99 0 99 99 99 99 #Missing data



0593095A97A02FCC
s/n = MDMS4121I