Question: Any User-Friendly (With Gui) Programs For Computing Watterson'S Estimate Using Sequence Data?
0
gravatar for Sang Chul Choi
4.7 years ago by
Sang Chul Choi0 wrote:

Hi,

I usually compute Watterson's estimate or other similar ones by hand or using calculator or by programming. Are there GUI (windows in mac, windows, or X-windows) computer programs people often use to compute those estimates with sequence data or genetical data (allelic data)? I want to let some people know those kinds of computer programs.

• 2.4k views
ADD COMMENTlink modified 4.7 years ago by Giovanni M Dall'Olio26k • written 4.7 years ago by Sang Chul Choi0
6

Did not you already write that program ? https://github.com/goshng/Mauve-Analysis/blob/b562564eab00f4b1f4d4827eeec50aef4f729af3/src/utils/compute_watterson_estimate.cpp

ADD REPLYlink written 4.7 years ago by Pierre Lindenbaum114k
5

There's a TV show in there somewhere, reuniting coders with their long lost repositories.

ADD REPLYlink written 4.7 years ago by Daniel3.7k

Ah... I do not even remember it. Thank you! But, I still want to know if there are other programs (nice one), so that I can just let someone who has no ability of programming or access to unix or windows. They would not know about programming, commands. They can use execute windows or GUI programs in windows, mac, or X-windows. Thank you for the link.

ADD REPLYlink written 4.7 years ago by Sang Chul Choi0

I edited the title and my question. Thank you for the answer, though. By the way, I often find your answers in Biostar extremely useful.

ADD REPLYlink written 4.7 years ago by Sang Chul Choi0

Never heard of it, but the formula looks very simple so it probably wouldn't take many minutes to program it..

ADD REPLYlink written 4.7 years ago by 5heikki7.8k

I want to know if there are such program or not. It is for someone who cannot program.

ADD REPLYlink modified 4.7 years ago • written 4.7 years ago by Sang Chul Choi0
0
gravatar for Neilfws
4.7 years ago by
Neilfws48k
Sydney, Australia
Neilfws48k wrote:

There is a R package, pegas, which includes a function theta.s() and references Watterson (1975).

ADD COMMENTlink written 4.7 years ago by Neilfws48k

Thank you for the anwer. But, R is still considered to be a programming environment.

ADD REPLYlink written 4.7 years ago by Sang Chul Choi0
1

Create a desktop GUI application.

ADD REPLYlink written 4.7 years ago by Ashutosh Pandey11k
1

Well, your original question included the phrase "command line", which I took to be shorthand for "comfortable running R" :)

ADD REPLYlink written 4.7 years ago by Neilfws48k
0
gravatar for Giovanni M Dall'Olio
4.7 years ago by
London, UK
Giovanni M Dall'Olio26k wrote:

You can try DnaSP, although the software is a bit old and I am not sure it will run on modern systems.

I would also look at Arlequin (maybe the Watterson's estimate will be in one of the logging files), and MEGA.

ADD COMMENTlink written 4.7 years ago by Giovanni M Dall'Olio26k
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