I am a real beginner in bioinformatics and need some hints. My data are mtDNA sequences in the AB1 format. My aim is to compute the Fst to get some insights in the population differentiation between two populations. It would be really nice to have all the computation in R, so I would need to know the right packages to read in and align the sequences and calculate the Fst.
Look at this link martin:
http://cran.r-project.org/web/views/Genetics.html
I hope you will find some useful relevant R pkg.
Dear Martin,
You may find the sangerseqR package from Bioconductor useful. In addition to CRAN, you will also find Bioconductor to be extremely helpful for analysis of biological data in R.
http://www.bioconductor.org/packages/release/bioc/html/sangerseqR.html
Briefly, there here are commercial packages (eg Stargene" and there are free packages like the above mentioned. Your can choose based on your budget and the requirements. I hope this answer may help
Dear Martin,
I think you would need to subdivide your task into three subtasks:
1) Convert the AB1 files into plain sequences (fasta).
2) Make a multi-alignment of the fasta sequences.
3) Compute Fst from the aligned sequences, e.g with Arlequin or software alike.
If this can all be done within R I am not sure (probably it can), perhaps indeed with Bioconductor.
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