I'm completly new to this programming/coding aspect in bioinformatics, althrough I'm quite successful using phylogenetic software for 2 years.
I'm planning a PhD project in which several open access tools are combined into one working pipeline/workflow/software (similar to MEGA5) to run analyses over night/week/month. Manually, this workflow cost me 1 year to analyze a bunch of proteins and to get familiar with several tools. For the long run, I want to implement this for a automatic sub proteome analysis.
Is it with any language possible to program a tool which is able to obtain data from a certain database, subject it to software A, control software A, send the output of software A to software B, control software B and so on?
The general workflow is mainly linear or has just one branching point.