jsdoublel / disco Goto Github PK

Hi,

I am unsure whether this is a good place to ask about the DISCO paper. I am trying to locate Sections S1 and S2 of the Supplementary material of the paper:

Willson J, Roddur MS, Liu B, Zaharias P, Warnow T. 2021. DISCO: Species Tree Inference using Multicopy Gene Family Tree Decomposition. Systematic Biology [Internet] 71:610–629. Available from: https://www.semanticscholar.org/paper/c2e21361ab0916cea8dee36891c6bc3c929c624d

I had a hard time locating tables in the Supplementary material as well.

Anyway, the following is the excerpt where I am confused.

Experiment Overview
Full details (including software version numbers and commands necessary to reproduce the experiment) are provided in Sections S1 and S2 of the Supplementary material in the paper.

By the way, thank you for the great work, DISCO.

SangChul

Hello James,
I've been using DISCO to resolve a set of multicopy gene trees. I noticed that a big portion of the trees are not resolved because they have less than four species (they don't meet the minimal species criterion). But, I also noticed that a small portion (~1%) of the trees have between four and six species and DISCO failed to produce a resolved tree. Here's an example...

Tree 81: Tree has 6 species.
Best root had score 792 with 778 duplications; there were 3 ties.
Outgroup: {Me_px_Sstr_Streblomastix_strix}
Decomposition strategy outputted 0 tree(s) with minimum size 4 .

Do you know a reason why this is happening?
Thank you very much!

Hi,

is there an easy way to get a partition file for the concatenated alignment made by ca_disco.py?

best,
Linde