Isolation by Distance Web Service

Isolation By Distance

Web Service

DNA Data

Version 3.16

Written by Andrew J. Bohonak and implemented by Eric Ngan, Julia Turner, Yoko Suzuki and Jeff Jensen with the aid of Scott Kelley

bohonak@sciences.sdsu.edu ericcngan@gmail.com juleigha27@gmail.com jljensen@stanford.edu skelley@sciences.sdsu.edu

Contact Eric Ngan for questions regarding usage, datasets, and problems associated with webpage.

Estimated Samples of Request Processing Times

1. INPUT DATA Important input data information!
Sample Data

Input Data Filename:

OR Paste Data:

2. BASIC SETTINGS

Number of randomizations (1-30,000):
For IBD plots, would you like a background grid?
Also perform analysis on Logarithmic (Genetic Distance)?
Also perform analysis on Logarithmic (Geographic Distance)?
Use negative genetic distances? (Otherwise, they will be set to zero.)
When log-transforming (genetic distance), negative genetic distances will be:	Set to value below Thrown out
When log-transforming (genetic distance), set genetic distances of zero to:
Calculate RMA regression residuals?

3. DNA DISTANCE SETTINGS

Genetic distances between populations:	Traditional FST PhiST (Incorporates sequence distance information)
Genetic distances between sequences:
Unknowns ('N' or '?') treated as:	Match to everything Missing data (ignore the site)
Gaps ('-' or ':') treated as:	Transitions (K2P distances, fifth state otherwise) Transversions (K2P distances, fifth state otherwise) Ignore gaps
Treat consecutive gaps as one:	No Yes

4. DETAILED IBD SETTINGS

Analyze IBD with:	Genetic distance FST (or PhiST, if chosen above) Slatkin's Similarity index M=((1/FST)-1)/4 or M=((1/PhiST)-1)/4 Rousset's distance measure FST/(1-FST) or PhiST/(1-PhiST)
If two populations are fixed for the same allele, FST or PhiST cannot be calculated. (There is no variance, so F is undefined). In these cases, what value should be substituted for FST or PhiST? (Should be 0, or at least smaller than all other values, if you want to assume that the populations are identical.)
If F <=0, genetic similarity (M) is infinity. What value should be used for M[max]? (Should be slightly larger than the second highest M; you may need to return to this screen and change M[max] after examining the scatterplots.) This value will also be used if two populations are both fixed for the same allele.
If calculating Rousset's distance, what should genetic distances of 1.00 be set to? This value will also be used if two populations are both fixed for different alleles.
Calculate summary stats for each locus? (>1 locus in development)

5. SUBMIT

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