GeneRax Species Tree Parsing Error

[Ankit Thakur]

Respected All 🙏,

I hope this email finds you well.

I am a PhD scholar in Computational Biology, and my research project is nearing completion. However, I am currently facing an issue while using GeneRax for gene tree and species tree reconciliation.

I have prepared all the necessary input files, including the alignment file, mapping file, starting gene tree, and species tree. However, when I run GeneRax, I encounter the following error:
[Error] Cannot parse species tree file (/home/ankit/Downloads/species_nameForTree (1).nwk)

Could you please guide me on how to resolve this issue? Any insights or suggestions would be greatly appreciated.

Thank you for your time and support.

 Best regards,

Ankit Thakur
PhD Scholar
CCBB LAB, CUHP

[Benoit Morel]

Hello Ankit,

To be on the safe side, I would remove the space in the file name and check again. If it still doesn't work, can you please send me the species tree file? It has to be binary and rooted

Best,

Benoit

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[Stefan Flaumberg]

Hi Ankit,

I'm almost sure that the error is caused by some problem with data, not by a bug of GeneRax. Without your tree file at hand, however, it's hard to tell what exactly has caused the error.

But you can check the tree file for the most obvious flaws yourself. To this end please: 

1. Try to rename the tree file, so that there are no special characters you have to escape with "\" (it should not be the error cause, but give it a try: rename it, for exapmle, to test_species_tree.nwk).

2. Make sure the species tree is rooted. If you reconstructed the species tree from a concatenated alignment with some phylogenetic tool, it is most likely unrooted.

3. Make sure the species tree is strictly bifurcating. There should be no trifurcations (such as in an unrooted tree, e.g. (1,(2,3),(4,5)); ) or monofurcations (might happen if you pruned it badly, e.g. red parentheses should not be here (1,((2,3))); ).

Best,

Stefan