Add --sequence option

[Wytamma]

This would allow users to replace the sequence/trait data using -DF and a JSON file.

dynamic-beast --sequence beast.xml 

Resulting in a dynamic XML file that has the sequence data replaced with $(sequence) and trait replaced with $(trait). The user can then specify these in a JSON file.

{
"sequences":"
<sequence taxon='D4Brazi82'>            ATGCGATGCG        </sequence>
<sequence taxon='D4ElSal83'>            ATGCGATGCG        </sequence>
<sequence taxon='D4Thai84'>             GTGCGATGCG        </sequence>
","trait":"
D4Brazi82  = 1982,
D4ElSal83  = 1983,
D4Thai84   = 1984"
}

This file would be run with beast as folows.

beast -DF dynamic.json dynamic.xml