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What do you think is the best language for Bioinformatics?
Hello
Please could you advise me what is the best language to use to perform statistical analysis on bioinformatics data (e.g. distribution of SNPs in a genome)?
I was going to use biojava because I come from a programming background and I like object oriented programming; plus the language has features for counts and distributions. However I have heard of R and know it is a language for doing statistics but I don't know if it is a 'fully fledged programming language'. For example, can you retrieve data from mysql databases or call web services or call, for example, a perl api of a bioinformatics resource from R? I know you can do these things or java. Or perhaps I could write my main program in java and call R routines to perform statistical functions. Or perhaps that it is just crazy and would involve too much passing to and fro.
It also seems that every bioinformatician uses perl or python so I feel like I'm doing something wrong by not learning one of these!
Many thanks in advance