OMA

[cyxiang1027]

I am using OMA to construct influenza virus-related gene sets. I downloaded CDS sequences at the family level from GenBank and RefSeq. When I run OMA, I encounter an error.
Reading 5873 characters from file Cache/DB/s108107.db
Pre-processing input (peptides)
12 sequences within 12 entries considered
Building new Pat index in file Cache/DB/s108107.db.tree with 4820 entries
Pat index with 4820 entries
sorted, from "AAAPPEQSRLQFSSLTVNV" to "YYLEKANKIKSGKTHIHIF"
Error, (in GenomeSummary) missing 5LETTERNAME in header part

[sinamajidian]

Hi!

Thanks for using read2tree. I'm wondering whether you followed the wiki step by step?
How many genomes/proteoems you are using? OMA is used to generate the reference gene markers, I guess 10 to 100 viruses should be enough.

Best,
Sina

[cyxiang1027]

I followed the steps mentioned above and downloaded more than 100,000 CDS sequences, using all of them. I want to obtain all influenza virus-related gene markers. If a species has multiple reference genomes, how should I choose one？