MEGA is very good ,,,,, u can also try taxon DNA

http://taxondna.sourceforge.net/

Thanks

I try MEGA but can't get the number of comparisons (combinations) for each species separately. If you know how to do it can you please let me know.

I ll try taxon DNA

DnaSP might be an option, if you are interested in intraspecific nucleotide diversity http://www.ub.edu/dnasp/

If you're just looking for the number of comparisons it's a simple mathematical problem. I don't know how to do equation notation in this interface, but it's the sum (n sigma i=0) of ni-1 where n is the number of sequences or taxa. For calculating the actual distances, both of the previously suggested programs should be able to give them to you - Mega will give you a pairwise matrix of distances, or if you designate groups of sequences it will give you group averages.

Actually I am interested in the number of combination. Using the example above for Species A there will be 3 combinations and for Species B it will be 6 combinations. For species A, the formula is 3C2 (3 is the number of specimens within the species and 2 is the pairwise comparison carried out) = 3 combinations of pairwise comparison

Similarly for species B, formula is 4C2 = 6 combinations

What I like to know if there is a software which can give me these combinations?

I used MEGA but cannot get the number of combinations. If anyone knows how to do it in MEGA let me know

I don't think you're going to find one. As far as I know most programs don't bother to report it because it's a simple mathematical calculation. If x is the number of comparisons, then x=(the sum of n-1) for all iterations of n, where n is the number of sequences.

x=0 for n=1. (ie. n-1=0

x=1 for n=2. (ie. n-1=1. So 0+1=1)

x=3 for n=3 (ie. n-1=2. So 1+2=3)

x=6 for n=4 (ie. n-1=3. So 3+3=6)

x=10 for n=5 (ie. n-1=4. So 6+4=10)

etc.

If you don't want to do the summation by hand you can calculate it easily in Excel. It's just x from the previous comparison plus n-1.

If I get it right then the different combinations will look like this:

---------------------No of sequences (n)----------------No combinations (C)

Species A ---------------------- 3 -------------------------(n-1)+(n-2) = 3

Species B ---------------------- 4 ------------------------ (n-1)+(n-2)+(n-3) = 6

Species C ---------------------- 2 --------------------------(n-1) = 1

Species D---------------------- 4 ------------------------(n-1)+(n-2)+(n-3) = 6

Species E -------------------- 5 ----------------- (n-1)+(n-2)+(n-3) +(n-4) = 10

Species F --------------------- 1 ------------------------ (n-1)= 0

Total combinations -------------------------------------- Σ C = 26

However to implement it in Excel is quite tedious as you ll have to change the formula each time

I believe that if using the formula (n(n-1))/2 will be much easier and can be implemented in Excel

---------------------No of sequences (n)----------------No combinations (C)

-----------------------------------------------------------------------(n(n-1)/2)

Species A ---------------------- 3 ---------------------------------------3

Species B ---------------------- 4 ---------------------------------------6

Species C ---------------------- 2 ---------------------------------------1

Species D---------------------- 4 -------------------------------------- 6

Species E --------------------- 5 ------------------------------------- 10

Species F --------------------- 1 --------------------------------------- 0

Total combinations ------------------------------------------------- Σ C = 26

Then the total combination can be easily work out as Σ (n(n-1))/2 where n >=1

In one of the discussion someone mentioned that the combination can be tabulated using MEGA, that's why I am asking if there is a phylogenetic software which can implement the combinations for intraspecific variations. If not then I presumed I have to export the genetic distances data as Excel file and thereon worked with them

Yes that's right. Since it's a static relationship it's easiest if you just make a table for yourself and look it up (which you can do with Excel) rather than calculating it each time. Mega will report the number of sequences in the comparison (which I realize is fairly trivial information, but is a pain to count by hand for large numbers) so then it's just a matter of consulting your reference.

One thing that's not at all clear is why you'd actually want this info? I have no idea what you'd use it for. The genetic distances themselves are easy to export as an Excel table if you need to do further manipulations of them, and Mega will calculate average distances for groups of sequences, including corrections for phylogenetic relatedness, without you needing to know the number of comparisons.