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Description
Nexus files support a translate directive in the trees block, which allows mapping short sample ids to full names. BEAST uses them, for example:
Begin trees;
Translate
1 Gorilla,
2 Homo_sapiens,
3 Hylobates,
4 Lemur_catta,
5 M._fascicularis,
6 M._mulatta,
7 M._sylvanus,
8 Macaca_fuscata,
9 Pan,
10 Pongo,
11 Saimiri_sciureus,
12 Tarsius_syrichta
;
tree TREE1 = ((((((1:8.539364784844837,(2:5.97056745117597,9:5.97056745117597):2.5687973336688668):12.369406882406174,10:20.90877166725101):5.9847286187282265,3:26.893500285979236):21.11768348386113,((5:6.112091996272027,(6:1.9410612498662478,8:1.9410612498662478):4.171030746405778):4.238726956087251,7:10.350818952359278):37.66036481748109):17.830130560055792,11:65.84131432989616):20.354509510375422,(4:63.14102590761508,12:63.14102590761508):23.0547979326565):0.0;
Would tskit be open to adding this functionality to the as_nexus method? It could be implemented with a node_labels parameter (same as in as_newick). If it's present as_nexus would output a translation table for node ids present in node_labels
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