single copy orthologue sequences using nucleotide sequences

[sowptika]

Hi David, Thank you for your previous reply. I would really appreciate your help if you could clarify my following doubts:

1. Can orthofinder produce single copy orthologue file using the nucleotide sequences (file having the CDS)?
2. Can it produce a phylogenetic tree using just the single copy orthologues after a MSA with MAFFT? If so, please help me with the process and the command line. I want a phylogenetic tree with only the single copy orthologue genes using the nucleotide sequences and not the protein.

Looking forward to your help. Thank you in advance.

Best Wishes

[davidemms]

Hi

If you use the option "-M msa" then it will infer a species tree with a concatenated multiple sequence alignment of single-copy genes. These are genes which are single copy in x% of species (but may be absent or multi-copy in the remaining species - any multicopy genes are excluded so that only single copy orthologs are used). OrthoFinder will determing the optimal value for x and will print it to the terminal when inferring the species tree. The process for species tree inference is explained here: https://github.com/davidemms/OrthoFinder/#species-tree-inference

You can do this either by supplying amino acid or nucleotide sequences as input.

Best wishes David

[sowptika]

Hi David, Thank you for your reply. Your answer could clarify my doubt but I have another query related to your reply. In the GitHub it is explained that if n (single copy orthogroup) >1000 then stop here. Does this mean if I have more than 1000 Single copy orthogroups it wont be considered for tree analysis?

Also I am having issue with hard and soft limits. My analysis required 10100 as limit and my hard limit is 10100. The soft limit has been increased to 10100 as well. But the tree could not be constructed. Do I have to increase my hard limit further?

Looking forward to your response Best Wishes Sowptika

[davidemms]

Hi Sowptika

If n>1000 then that if fine, it means it has lots of data.

You say the tree could not be constructed, do you have information that suggests it is related to your limits? The best thing is to post the complete output from OrthoFinder as that should contain the information to identify the problem.

Best wishes David