I am studying the genetic diversity present in a collection of accessions for a few specific genes. I have VCF files as input data, and I am trying to use the R package 'pegas'. It seems really useful and straightforward, but the only issue I am having is because I am starting with VCF files instead of FASTA files. Do you have any advice? Is there any other package in R which would allow to work with VCF easily? Would it be best to generate first the sequences for each individual in FASTA format before starting the phylogenetic analysis?
Any suggestion is welcome. Thank you.
I suggest you use the fasta format to generate the sequence first. Then align the sequence using mega or other software then you can easily infer your phylogenetic tree.
You can also use network software apllications and the DNAsp to do your haplotype analysis and maternal lineage analysis.
Hello,
please have a look at the following link,
https://cran.r-project.org/web/packages/vcfR/index.html
https://grunwaldlab.github.io/Population_Genetics_in_R/reading_vcf.html
Best regards
Thank you both for your answers. I will take a look at the software and packages you suggested.
Best regards!
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