problem with SingleCopyOrthogroups

Question

[imda]

Hello, I have run Orthofinder successfully. However, I am a little bit concern about my results. I have to say that I am very new at this. When I look out the file SingleCopyOrthogroups.txt I just found 78 orthogroups, and since my point of view, I do not know if they are very few or what?

These are the overall statistics

Number of genes 464039 Number of genes in orthogroups 398925 Number of unassigned genes 65114 Percentage of genes in orthogroups 86.0 Percentage of unassigned genes 14.0 Number of orthogroups 26588 Number of species-specific orthogroups 597 Number of genes in species-specific orthogroups 2888 Percentage of genes in species-specific orthogroups 0.6 Mean orthogroup size 15.0 Median orthogroup size 13.0 G50 (assigned genes) 22 G50 (all genes) 18 O50 (assigned genes) 5348 O50 (all genes) 6973 Number of orthogroups with all species present 8292 Number of single-copy orthogroups 78 Date 2019-02-25

I want to run CAFE, but I do not know if the Species Tree that was constructed with only 78 single-copy Orthogoups is enough

I used the option -msa (MAFFT and FastTree).

Thanks

Answer 1

[shelkmike]

How many single copy orthogroups you get depends on how phylogenetically distant your species are (the more distant, the less single copy orthogroups you will have) and also on how good the genome assemblies are. Based on my experience, 78 single orthogroups is not bad. This may be enough to create a proper phylogenetic tree. What I suggest is to concatenate all these 78 alignments, remove poorly aligned regions by Gblocks, then build a phylogenetic tree with bootstrap analysis (I prefer RAxML for this) and look at whether your bootstrap support values are high.