I have some experience, through teaching myself, of using R for RNAseq, ChIPseq etc, but have started in a new field of research. Specifically I am working with bacteria and would like to, for example, be able to align specific regions of AminoAcids (which is used to split the bacteria I am studying into sub-strains).
I have begun to play around using R and packages such as DECIPHER to import reference train sequences in FASTA format, translate them and do alignments. But I need some way of speeding up my learning curve as I can not spend as long as I did in my PhD learning and trialling packages etc.
So the question really is does "the biostars handbook" provide this kind of information, with a practical section to get me started understanding and building phylogenetic trees from alignments?
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Much of the analysis methodology is classic. You can take a look at this older review to get a start. If you need an easy to use program give MEGA a try. There is background material and tutorials on MEGA website.