bruvo.boot

[Sakthipriya M]

Hello All,

1) I like to use the below code to create the distance tree for my mixed ploidy data analysed using SSR markers.  I am not sure how to add a repeat motif length number? 

Example:

SSR1 - (CT)15,  SSR2 - (CA)10,  "SSR3- (AG)5(AG)8,  SSR4- (TC)23(TA)7" 

mydatafr <- c(15,10,?,?)

Shall I add both n repeats -  5+8 =13; 23+7=30 and use c(15,10,13,30). or take average of both (ie) SSR 3 - 6.5, SSR 4 - 15 c(15,10,6.5,15)? Is this correct ?

## below code

mydatafr <- c(15,10,..... ) 

geneticdistancetree <- bruvo.boot(mydata, replen = mydatafr, cutoff = 50, quiet = TRUE)

 

2) Is there any option in poppr to calculate inbreeding coefficient, probability of exclusion of identity and paternity (I and Q) for Microsatellite markers?

Kindly help to solve this and Thanks 

-  Sakthi

[Zhian N. Kamvar]

Hello,

1) The way you are defining the repeats is not exactly correct. You want the length of the motif (CT), not the length of the sequence (15). Bruvo's model assumes that you do not have mixed motifs, so any model you choose will be wrong. For the repeats you've shown, you may want to take the average of distances at 2 and 4 nucleotides or just set it at 3 nucleotides.

2) No. But you can use the hierfstat package. That has options for calculating inbreeding and will take the genind object as input.

Best,

Zhian

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