Add phylogeny and read alignment visualisation

[monicadragan]

Implementation details:

Add visualization putput for philogeny and read alignment (now there are 2 html outputs: snv_calling.html and alignment.html).

• for the phylogenetic tree: (1) compute MSA and the tree with augur tools, (2) display the tree in nwk format using the phylotree.js library (I copied with reference the necessary js code in the visualisation html file)
• for the read alignment: I used IGV.js webapp - I use igv-reports to converts the FASTA and BAM input files to a data uri that will be used to call the library. This results into stand-alone javascript code that can be integrated in the visualisation html file.

[DrYak]

Merged into rubicon's #9371461 :confetti_ball: !