Add support to export distances as pairwise distance matrix

[huddlej]

Context

MicrobeTrace supports visualization of genetic relationships based on pairwise distance matrices (see also this tutorial video). A long-standing request from the MT team has been for augur distance to export distances in this pairwise matrix format, so users could easily create a matrix from an alignment and view in MT.

Description

Supporting pairwise distance output would make the most sense when users run augur distance with the --compare-to pairwise argument.

augur distance has a complex interface with many options to compare input sequences to each other or the root sequence or a recent ancestral sequence. The interface also allows users to pass multiple distance maps with different compare-to arguments and attribute names and saves those attribute-named outputs as keys in the JSON output file.

The distance matrix output format only would only work for one distance map/attribute at a time. If we added an optional --output-distance-matrix argument, we would need to either require a single distance map input for a single output file or we would need to allow the number of outputs to match the number of distance map inputs for pairwise comparisons.

Exporting a pairwise distance matrix is probably the simplest part of implementing this feature. Deciding on and implementing a reasonable user interface on top of the existing augur distance interface is more complicated.