Both the methods are having their own advantages and disadvantages. If u have allelic data you can use it. Tree construction is not same in every method and u shd have knowledge of the crop/animal/other things on which u r working and then see whether ur hypothesis is coeing true based on tree constuction. The trees will be diffrent. If u want to have confidence in trees then go for bootstrap

@ Anil K

Thank you for you kind response.

1. Ya got the result with respect to trees and found the differences in trees as you said.

I found difference in(in between-inter) the clusters but not between( intra) the clusters.

2. I tried with different boottraps 100,1000 and 5000 and even I found the result as above.

3. I have few more questions with respect to scoring and analysis

a. scoring the data is, better for 0/1 or in terms of bps(100 bps,150bps ) etc for SSR marker scoring ?

b. can we interpret both phenotypic and genotypic data to get one tree ?

c. For tree construction weighed/ unweighted is better?

thank you.........

You must to do a binary matrix (0-1) looking on the position of each band according to the size in bps. In my opinion, you can not do the analysis together, is better to do each one separately and of course, you will see different results or maybe you can cluster two different genotypes in the same node following the phenotype, whereas they can reach different node when you will be doing the genetic analysis by SSR, which is the most powerful tool to decide who are similar or not. For you last question, I prefer unweighted.

@ Aroldo C

Thank you for your nice explanation and even I will follow unweighted.....

if u have to interpret both genotypic and phenotpyic data u can do that. in NTSYSpc it can be done. In DARWIN i dont think it takes the phenotpyic values. u have to look for some other programme which takes both the values

Allelic data or 0/1 data u cna use anything

@ Anil K and @ Aroldo C

Thank you for your replies..

I have one more question for you peoples with respect to scoring

a. How enter the data for more no of alleles (1-4) in terms of 0/1 pattern.

b. How to score hetero zygotes in terms of 0/1 pattern.

thank you...

The only difference in the two is the input data type that you use. Single data uses Binary data (1) and (0) or any other data type scored from phenotypic traits or dominant markers. Allelic data analysis uses only genotypic/ allelic data which is in form of alleles in basepairs. There is a disadvatage of using allelic data analysis when you are dealing with polyploid data as this option only takes diploid data (not more than two alleles per SSR locus). I have comprehensively used these two data analysis for over eight crop species both of diploid and polyploid nature.

Go ahead and score the SSR data as alleles in basepairs then use ALS Binary software (its free) to convert the data into binary data "1" where an allele is present and "0" where the allele is absent then use this as your input DARwin file.

@ Mercy K

Thank you for your response and giving information about the ALS Binary software. I downloaded it unable to work on it. please let me know the flow chart if you have.

thank you..

I believe Mercy has been able to give you a better approach to solving your problem. Why not try it?

@ Gbadebo O

I tried thats's what I mentioned above comment. I downloaded it unable to work on it because not able to feed the commands....

thank you...

Go to the internet and goggle ALS Binary software, many files will open but open the one written ALS Binary & Bingeno, reading downwards you will see "download", a window will open where you are supposed to enter your details, i think they do this not to charge but keep track on who is using the software. After entering your details click on download at the bottom of the window and you will see the software download create a folder in my computer C drive and save the software. . Format your data so that markers are columns and samples are in rows and save the file in tab delimited format and in the same folder with the software so that it can recognize it. then you are good to start, when you open the software and start it you are told to enter file name with an extension...e.g. TomatoSSR.txt

kindly let me know how this goes and all the best.

Note: 1. remenber to save the software and input file in the same folder

Thank you Mercy it's working now let me try it more.....

Am sorry for misleading you on the input data file, the input data file should all be in columns

marker...sample...allele1...allele 2....allele 3 but dont put an heading. if the samples have different number of alleles, fill the rest with 0 so that the number of alleles are equal in all.

Our article published in peer-reviewed Journal "Communicative & Integrative Biology". A few major points discussed in the paper:

(1) Brain is not the source of consciousness.

(2) Consciousness is ubiquitous in all living organisms, starting from bacteria to human beings.

(3) The individual cells in the multicellular organisms are also individually cognitive entities.

(4) Proposals like “artificial life”, “artificial intelligence”, “sentient machines” and so on are only fairytales because no designer can produce an artifact with the properties like internal teleology (Naturzweck) and formative force (bildende Kraft).

(5) The material origin of life and objective evolution are only misconceptions that biologists must overcome.

http://www.tandfonline.com/doi/full/10.1080/19420889.2015.1085138