Invalid mapping can't find the gene in the gene tree can't find the species in the species tree

[junyuan li]

Hi Dears, 

I am using the Generax 2.0.1 to correct the gene family tree, while I have checked many times about the inputs files there is still error reports:

[00:00:00] Filtering invalid families...

[00:00:00] Starting species tree initialization...

[00:00:00] End of species tree initialization

[00:00:00] Filtering invalid families based on the starting species tree...

[Error] Invalid mapping <->: can't find the gene  in the gene tree

[Error] Invalid mapping <->: can't find the species  in the species tree

Error in family family_pax: Failed to map genes and species

WARNING!!! Found 1 invalid families (they will be discarded from the analysis)

[Error] No valid families! Aborting GeneRax

My command is :

generax -f families.txt -p generax -s speciestree.treefile --rec-model UndatedDL --max-spr-radius 5 

My inputs are attached.  

Would you please help check what is wrong with it? 

Thanks a lot!

Li Junyuan

[Benoit Morel]

Dear Li Junyuan,

Thanks for your report. This is apparently due to the empty line at the end of your mapping file. If you remove it, everything should run smoothly.

I will try to make the parser more permissive in the next release.

Best,

Benoit

[junyuan li]

Dear Benoit,

Thanks for your promptly reply! According to your instruction, the program ran smoothly, and the result files were produced. However I confronted another problem to ask your help.

My main purpose of using Generax is to produce a more confident gene family tree, considering your software taking the species phylogeny into account. However, when I entered the /results/family_pax or the /reconciliation directory, neither the geneTree.newick nor the family_pax_reconciliated.nhx has bootstrap values (only branch length presented). Would you please see what is the problem?

Best wishes,

Li Junyuan

2021-5-12

[Benoit Morel]

Dear Li Junyuan,

As I explained here (https://github.com/BenoitMorel/GeneRax/issues/52), GeneRax doesn't produce support values yet, because the classic bootstrap technique cannot be applied to our joint model. I have the project to adapt this technique to GeneRax, but I haven't had the time to work on it yet.

If you have the species tree, GeneRax is more likely to produce a more accurate gene tree than "just" raxml or iqtree, but, so far, we can't assess the confidence in the gene tree. Maybe you could somehow compare the generax tree with a raxml tree (which can have meaningful support values), and look at how much they differ?

Best,

Benoit