RANGER-DTL ERROR: missing ')' in input tree expression line x column xx

Question

[seok1213neo]

I am working on RANGER-DTL to see some horizontal gene transfer events.

I downloaded the linux file of RANGER from their website, and I did the following command

./OptRoot.linux -i group_1.newick -D 3 -T 4 -o outcome.txt

and i got

Input file: group_1.newick
Output file: outcome.txt
Duplication cost: 3, Transfer cost: 4, Loss cost: 1
Random seed: 23871
ERROR: missing ')' in input tree expression line 1 column 66

it seems like my newick files are okay after I saw them through a website tree viewer, the website was able to construct trees out of it.

could anyone please help me solve this prob?

thnks!

[ganesh]

Hi @seok1213neo . Were you able to find a solution for this? I am facing the same issue with RangerDTL with version 2.0. The gene and species trees seem to be fine. The previous versions had issues with special characters in the tip names. But that should be resolved in the latest version. However, I have removed all the special characters from my trees and still facing the same problem. Please update if you have found a way to solve this! Thanks GM

Answer 1

[philipgdv]

Hi, I ran into the same issue and managed to solve it. Someone reported a similar issue on the github repo of MetaCHIP. My newick files contained branch lengths written in scientific number format, with a hyphen ("-" in 2.5e-06), which RANGER doesn't support. Replacing them fixes the issue. Hope it helps!