Refactored multiple align to isolate alignment from tree browsing logic,
and wrote a logic to browse scipy-style linkage matrix + tests +
updated deps

 * Raw timings for the pairwise alignment of the first two sequences of
   each balibase file
 * Timings for alignment of mouse and human titin, with a timeout
   controlled by `UNIT_TIMEOUT`

 * Forgotten an in-place modification of arguments in `align`
 * Wrong initialisation of first column in `align` (index confusion)