msci input format #203

mprebus · 2025-01-14T19:23:11Z

Hello, I am attempting to run a complex introgression model, but I have run into issues specifying the extended Newick tree. The msci generator makes the tree without problems, but I am receiving an error message when I attempt to run it:

[ERROR] Parental nodes of hybridization b have an ancestor-descendent relation, but the ancestor has no tau paremeter (tau-parent=no)

msci.txt
bpp.ctl.txt

xflouris · 2025-01-16T00:35:00Z

Hi @mprebus ,
there is a problem with the introgression model you are trying to create.
You have the following definitions in the msci.txt file:

tree (R,((A,V)q,((T,(C,Y)r)s,((M,(P,D)n)u,(B,L)v)w)x)y)z;
hybridization x w, s T as a b tau = no, yes phi = 0.5
hybridization b T, w v as c d tau = no, yes phi = 0.5 
bidirection w u, x s as e f phi = 0.5, 0.5
bidirection x a, x f as g h phi = 0.5, 0.5

Now consider the picture below that depicts the binary tree and the first two hybridization commands:

The a->b introgression corresponds to: hybridization x w, s T as a b tau = no, yes phi = 0.5
and c->d to: hybridization b T, w v as c d tau = no, yes phi = 0.5

By introducing the first introgression (a->b) you explicitely indicate to the program that s is older than w.
The issue arises when you add the third event: bidirection w u, x s as e f phi = 0.5, 0.5.
This implies a bidirectional introgression between edges w-u and x-s. However, these two segments are not contemporary because based on a->b, s is always older than w.
This is what essentially the error message tells.

mprebus · 2025-01-16T16:23:37Z

Thank you, that makes sense. Should have plotted it out myself!

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