taking dna/CDS sequence as input

[baoxingsong]

Hi David,

I tested OrthoFinder on several well-assembled species, it works very well. Now I am working on several species with genome sequence being assembled using only nanopore reads. There is a high error rate and this would affect protein sequence a lot.

So I want to take the CDS or DNA sequence as input to find orthologous. Could OrthoFinder take DNA sequence as input, please? Or do you have any recommendation, please?

Baoxing

[davidemms]

Hi Baoxing

It's something I'm going to be working on over the next few months. There's nothing ready yet but I'll post here when there's something available.

All the best David

[ViriatoII]

Any developments? :)

[haruosuz]

Dear David: I look forward to the next version of OrthoFinder which can take nucleotide sequences as input.

[ViriatoII]

Dear David: I look forward to the next version of OrthoFinder which can take nucleotide sequences as input.

It's here!

[davidemms]

Thanks for the post/reminder. Yes, it's in the latest release.

[HendAbuElmakarem]

Hi David

I have used Orthofinder on DNA sequences and I would like to confirm whether the inferred trees are from the nucleotide sequences or their translated proteins

Thanks Hend

[haruosuz]

Dear @davidemms

When the option -d (Input is DNA sequences) is used, BLASTN search is performed on the DNA sequences (or the DNA sequences are translated for BLASTP search)? For each orthogroup, multiple sequence alignment (MSA) is inferred at DNA level (or MSA is inferred at amino acid level and then backtranslated to DNA) to infer gene trees?

[RijanDhakal2055]

@ViriatoII

It's here! I am trying to run orthofinder on DNA data but cannot find the right flags to do it. I have tried the following combinations: Orthofinder -d {folder with data} Orthofinder -d -f {folder with data} Orthofinder -f {folder with data} -d Orthofinder -fd {folder with data}

None are working and I cannot find the right flag for CDS data in the manual or google. Do you know the right ones? Could you let me know if possible?

[Estherrr1997]

@ViriatoII

It's here! I am trying to run orthofinder on DNA data but cannot find the right flags to do it. I have tried the following combinations: Orthofinder -d {folder with data} Orthofinder -d -f {folder with data} Orthofinder -f {folder with data} -d Orthofinder -fd {folder with data}

None are working and I cannot find the right flag for CDS data in the manual or google. Do you know the right ones? Could you let me know if possible?

Hey RijanDhakal2055, Did you find a way to use DNA data as input? I am trying to do the same but get an error message each time: 2022-09-06 13:12:23 : Creating blast_nucl database 5 of 6 2022-09-06 13:12:33 : Creating blast_nucl database 6 of 6

Running blast_nucl all-versus-all

Using 32 thread(s) 2022-09-06 13:13:15 : This may take some time.... 2022-09-06 13:13:15 : Done 0 of 36

WARNING: program called by OrthoFinder produced output to stderr

Let me know if you found a way to fix the error and use the DNA data! :D Would really appreciate it