NTSYS pc is a software that can help you discover patterns and structures in multivariate data, such as molecular genetic data. You can use it to transform data, estimate similarities or dissimilarities among objects, and summarize the relationships using cluster analysis, ordination, and multiple factor analyses. You can also construct phylogenetic trees using the neighbor-joining or UPGMA methods.
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In this article, we will show you how to use NTSYS pc for molecular biodata analysis in a few simple steps. You will need to download and install the software from here. The software is not free, but you can request a trial version or purchase a license.
- Calculating similarity or dissimilarity matrix. You can use the SimQual module to calculate the similarity or dissimilarity matrix among your objects (such as DNA sequences, genotypes, phenotypes, etc.). You need to input a file with your data in rows or columns, and choose a coefficient (such as Jaccard, Dice, etc.) to measure the similarity or dissimilarity. You can also choose to standardize or transform your data before calculating the matrix. The output will be a file with the matrix that you can save for further analysis.
- Performing cluster analysis. You can use the SAHN module to perform cluster analysis on your similarity or dissimilarity matrix. You need to input the matrix file and choose a method (such as neighbor-joining or UPGMA) to construct a dendrogram. You can also choose to plot the dendrogram on the screen or save it as a file. The output will be a file with the cluster information and a graphical representation of the dendrogram.
- Performing ordination or multiple factor analysis. You can use the PCO module to perform ordination or multiple factor analysis on your similarity or dissimilarity matrix. You need to input the matrix file and choose a method (such as principal coordinates analysis or correspondence analysis) to reduce the dimensionality of your data and display it on a scatter plot. You can also choose to rotate, scale, or label your plot. The output will be a file with the ordination or factor scores and a graphical representation of the plot.
These are some of the basic functions of NTSYS pc that you can use for molecular biodata analysis. For more details and examples, you can refer to the paper by Jamshidi and Jamshidi (2011) or the discussion on ResearchGate.
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In this section, we will show you an example of using NTSYS pc for molecular biodata analysis. We will use the data from a study by Mir Drikvand et al. (2015) on the genetic diversity of some durum and bread wheat genotypes using SSR markers. The data consists of 30 wheat genotypes and 10 SSR markers. The data file is available here.
- Calculating similarity matrix. We will use the SimQual module to calculate the Jaccard similarity matrix among the wheat genotypes. We need to input the data file in rows format, and choose Jaccard as the coefficient. We will save the output as a file named wheatjaccard.
- Performing cluster analysis. We will use the SAHN module to perform cluster analysis on the Jaccard similarity matrix. We need to input the wheatjaccard file and choose neighbor-joining as the method. We will plot the dendrogram on the screen and save it as a file named wheatnj.
- Performing ordination analysis. We will use the PCO module to perform principal coordinates analysis on the Jaccard similarity matrix. We need to input the wheatjaccard file and choose PCO as the method. We will plot the scatter plot on the screen and save it as a file named wheatpco.
The results of the analysis are shown below:
The dendrogram shows that the wheat genotypes can be divided into three major groups based on their genetic similarity. Group I consists of 22 bread wheat genotypes, mostly of winter growth type. Group II consists of five bread wheat genotypes, mostly of spring growth type. Group III consists of three durum wheat genotypes.
The scatter plot shows that the first two principal coordinates explain 67% of the variation in the data. The wheat genotypes are clustered according to their groups in the dendrogram, with some overlap between group I and group II. The durum wheat genotypes are clearly separated from the bread wheat genotypes along the first principal coordinate.
This example demonstrates how NTSYS pc can be used for molecular biodata analysis using simple steps and graphical outputs. You can try it with your own data and explore more features and options of the software. 8cf37b1e13