read a tree sequence into msprime ?

[eldonb]

hi all,
was wondering if it is possible to read tree sequence data into msprime ?

I am working on individual-based simulations that generate ancestral trees in two ways, and would like to
plot some example trees using the tskit draw_svg facility, and possibly for comparison with output from msprime;
so I have my own code for generating trees and once converted to tree sequence format read them into msprime ?

a simple example - for a single non-recombining locus I have an output (in compact form)
0 1 2
i i j
k k

meaning that I label the sampled leaves as 0,1,2; after (say) r generations the ancestors of leaves 0 and 1 merge, and after further (say) s
generations the remaining two ancestors merge; the tree sequence would then be (I reckon) <3,3, 4, 4, 0>
with node times (0,0,0, r, r + s)

so was wondering if it is possible to read tree sequences generated outside msprime into msprime ?

best
bjarki

[eldonb]

update: was viewing tskit and msprime as one and the same thing -
maybe a more accurate question is :
are there examples showing how to generate tree sequence data from scratch (even a made-up example,
not an output from any simulation software, and just in the simplest case of a single non-recombining locus, and only the bare-bones ancestral relations) that the tskit library can process, in particular plot trees ?

[GertjanBisschop]

Hi @eldonb,

Good starting points might be editing tables and building simulator with tskit. Especially the first link will highlight how you can modify/build the tables that underlie any tree sequence yourself. Once you get to grips with the fundamental building blocks it is relatively easy to code up your own example tree sequences and plot them.