Step by step process is as below

First fill excel sheet with Row A with 1 B with Number of Rows C with Columns and D with 9 (if missing data is there fill with 9)

From A 2 to An wirite 1 to n (markers) as column

From B2 to Bn your variables (example varities)

Then go to save as and save your file in text tab delimited (Remember to name it as example.nts)

Run edit from NTSYS and save the file

Run the cluster using Similarity and change Jaccord/Dice or any other then Compute

Go to Clustering and then to SHAN module and compute and save

Then go to tree to view

I have Bathch file which is very easy i will send you the same by monday

Step by step process is as below

First fill excel sheet with Row A with 1 B with Number of Rows C with Columns and D with 9 (if missing data is there fill with 9)

From A 2 to An wirite 1 to n (markers) as column

From B2 to Bn your variables (example varities)

Then go to save as and save your file in text tab delimited (Remember to name it as example.nts)

Run edit from NTSYS and save the file

Run the cluster using Similarity and change Jaccord/Dice or any other then Compute

Go to Clustering and then to SHAN module and compute and save

Then go to tree to view

I have Bathch file which is very easy i will send you the same by monday

Thanks Padder. I have attached the xls file....then I opened it in NTedit and save the file. My question is that after that I have to edit the file or directly open in NTSYS and in cluster analysis the coefficient (scale) showing four digit number. why it is coming like that?

Xls file

@B.A.: When you use newer versions of NTSYSpc, you are allowed to use NTedit (incuded in the NTSYS package) to create .NTS files directly from .xls. Biswajit, as I can see from the table attached, you placed you accessions properly in columns, while loci (having no labels) are placed in rows. In the dendrograd you attached, software clustered your loci instead accessions. You should follow the procedure: in the first place, you should label the loci in .xls file. When you import .xls in the NTedit software, make sure you have a Rectangular matrix with 36 rows and 20 columns. Save it under the chosen name (e.g. MATRIX.NTS) and start NTSYSpc. Now you should be able to see 5 cards (tabs): General, Clustering, Graphics, Similarity, and Ordination. To make a dendrogram with e.g. Jaccard's distances, you should make comparison between the accessions. Regarding binary matrix you attached, you should choose Similarity card and then click to SimQual. In opened window you have to locate your MATRIX.NTS file, uncheck "by rows", choose "J" from the drop-down menu (for Jaccard's distances), type the name (e.g. DISTANCES.NTS) and the location of the output file, and click Compute. After that, click on the Clustering card and choose the clustering algorhythm (for UPGMA, you should click on SAHN). Locate input file (DISTANCES.NTS), give a name to the output file (e.g. TREE.NTS), choose UPGMA from the drop-down list, all other paramethers leave as they are, and click Compute. Next: in the Graphics tab, click on the Tree plot and all you have to do is to locate TREE.NTS file. Here you go.

i Have a batch mode file. Kindly run your nts file. Keep this file in the folder where you have nts file. Name the file as X.nts. Open

Have a batch mode file. Kindly run your nts file. Keep this file in the folder where you have nts file. Name the file as X.nts. Open the batch mode and run it. in Case of any problem kindly send the excel file

I have done the analysis for you as an attachment. Kindly change the name of bose to x and run the batch mode using your ntysis. All the files are attached along with the tree. If you want to view the tree using Ntysis kindly go to tree and give input file as bose2

Many many Thankz PADDER......finaly I got the tree with desired result. Actually while importing exel file using OLE option in NTedit and i have to delete all letters "R" in front of R1 R2 R3 etc and save the file to be analize in NTSYS. Then, open NTSYS and import the save file, do not click " By rows" , then Jacard dont change anything and compute.

After that, click on clustering, then SHAN,then previously generated .NTS file ( from Jacard Similarity analysis), clustering method-UPGMA, FIND then Maximum No. of tied trees 25 (if my samples are near 25) dont change anything and compute....

I got the tree like you Padder.....Thanks a looot.

But, now, I have some questions....

What version you use?

Do you have to edit after importing the exel file using NTedit (the 1st generated .NTS file to be used in NTSYS pc) like me?????

Why did you use 9?? I didnt use 9 as I do not have any missing value?

After analyzing the similarity by simqual, the .NTS generated looks slight different...

I have attached the files....thanks a looot again for teaching me NTSYS pc...may I have ur email id....I have loot to learn.

Thankz Branislav Šiler... :)

I am using NTYsis 2.10z. It is similar to your version only difference is that you can directly import exl file (97-2003 Microsoft excel).

Yeh I have to use NT Edit option to import excel file and then save as

As far as similarity by simqual, the .NTS generated looks slight different...---- is considered it may only be because I used Jaccards coefficient and you may have used simple matching option (which is a default as SM)

Why did you use 9?? I didnt use 9 as I do not have any missing value?

if you do not have missing value use 9 integer if you write 1 or 0 it will treat them as missing

You are welcome.

My email id is [email protected] and you can contact me any time.

Try to use batch mode which is very easy as I have all the batch mode files for PCA, Cluster analysis and other analysis which NTYSIS does

Thanks sir....How to create batch mode file? I just used Jacard coeff and use 0 and got the tree like you Sir.

the batch mode files are written on note pad and then saved as .atb eg xyz.atb I have attached one file to you check that. It will not open as such. Either use NTYSIS to open or right click the file and then go to OPEN WITH and Select NOTE PAD

Remember you should name nts file what is written in batch file

Thanks a lot

Hi everybody

can i have one question about using ntsyspc 2.1. when i used this software to analysis genetic distance (GD) and genetic simillarity (GS) , for my understanding, GD + GS = 1 that is truth or not? in my GD result that got from using ntsyspc, it appeared value >1 can anybody explain that problem? many thank you

That's right, Nguyen, GD+GS=1. Are you sure you've fully followed the steps described above?

hi Branislav i follow step by step mention above. just dont know why that happen.i try to do which another sample but also got that problem？

Hi this software is freely available or paid?

how to interpret PCoA 3D scatter plot  generated by Ntsys for diversity analysis

Well, V.L., the basic purpose of the PCoA is to visually interpret genetic relationships among some samples in a  set. It reduces the number of variables in such manner that the first dimension in a 3D plot describes the greatest amount of the total variation, the second dimension less, and so on. So you should visually inspect is there any grouping of samples, what is the dispersion in a group, are potential groups separated from each other (particularly along the first axis) and make conclusions out of that.

Is it safe to download online free version of NTSYSpc 2.2 software

Dear B A Padder,

Could you please tell me how can I analyze replicated data (like population genetic diversity)? For example, I have 4 populations, each population has 50 samples, how can put this data in the input file?

Use Genalex

It is very easy. Send your personal email I can send step by step. My personal Email is [email protected]

Dear Sir Arup Kumar,

Please I am also very interested with the step by step use of NTSYSpc 2.02. If agreed, my personal e-mail is [email protected].

Many Thanks in advance!

Best Regards

Difo

Could you help me how to download free NTSYSpc software. some times i able to down load but asking password.

Ntsys is not a free software

I am satisfied with answer of Branislav Šiler. Thanks a lot.

Respected Sir Arup Kumar,

I want to use the NTSYSpc2.02 which will helpful for my data analysis and interested to learn with the step by step use of NTSYSpc 2.02. If agreed, my personal email is [email protected] . Kindly help me out..

Many Thanks in advance!

Best Regards

Ashish Gautam

you can purchased NTSYS-pc 2.02 software online it's about 400$

how to analyze the RAPD marker data for diversity analysis. I want to have PIC content

Suvarna Biradar I think you can use PopGen

there are different formula to calculate PIC. which one i have to use is confusing.

formula i referred in discussion in research gate and also compared with Liver pool PIC calculator. answer is different. RAPD marker i want correct formula.

Hi there,

I liked this discussion and wanted to know more about NTsys software. How can we plot 3D plots via NTsys? Is there someone that can help me get one 3D plot with my small data please? I do not have this software and need this plot please.

Thanks very much

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