4
votes
How to analyse Orthofinder results
I think they simply calculate the percentage of proteins in each species that belongs to an orthogroup conserved in the five species.
There should be a tab separated text file called Orthogroups....
- 81
2
votes
Accepted
expansions and contractions from OrthoFinder
The answer is actually right there in the error message (warning message, actually):
DtypeWarning: Columns (2,... 968) have mixed types. Specify dtype option on import or set low_memory=False.
...
- 9,662
2
votes
Accepted
Removing data from OrthoFinder output prefix
The latest version solves the issue.
Source : https://github.com/davidemms/OrthoFinder/issues/403
Latest Version: https://github.com/davidemms/OrthoFinder/releases/tag/2.4.0
- 76
2
votes
Error with eggNOG-mapper jobs
I'd like to answer my own question as I have found the solution for this and thought it might help anyone else trying to use eggNOG-mapper.
The prerequisite for uploading the input file with the ...
- 105
2
votes
Accepted
Error with eggNOG-mapper jobs
There is a known bug between eggNOG-mapper2 and eggNOG6. This is described here:
https://github.com/eggnogdb/eggnog-mapper/issues/428
In your case, I'm not sure on what strategy you are deploying ...
M__♦
- 11.9k
2
votes
Given a FASTA file with a set of genes, how do I determine that set's conservation among a genetic order?
It's possible that MOLE-BLAST could help for you:
MOLE-BLAST is an experimental tool that helps taxonomists find closest database neighbors of submitted query sequences. It computes a multiple ...
- 13.8k
1
vote
expansions and contractions from OrthoFinder
The error right at the end is
Specify dtype option on import or set low_memory=False.
Edit Oh wait @terdon has already spotted ...
M__♦
- 11.9k
1
vote
Accepted
How to add bootstrap values to the phylogenetic tree generated by OrthoFinder?
Bootstrapping is easy just use iqtree
iqtree -s file -m GTR+I+G -T 6 -B 1000
This will parallelise across 6 CPUs and results in 1000 bootstraps, whilst GTR is the ...
M__♦
- 11.9k
1
vote
Accepted
How to use Gblocks for trimming single-copy gene sequences?
Basically this is 16S data. If its proteins there's a different strategy - even if the data set needed is nucleotides (separate question). I would simply use trimal which is available on conda
...
M__♦
- 11.9k
1
vote
Accepted
No bootstrap value on single-copy gene tree created by OrthoFinder
Please check the file
`$PWD/SpeciesTree_unrooted.txt" `
You should find the bootstrap support* values per branch there. If not make sure is the latest ...
M__♦
- 11.9k
1
vote
Number of sing-copy genes identified by orthofinder is far less than BUSCO assessment?
It's hard to say for sure without seeing the exact commands you used. However, Orthofinder identifies/defines single-copy orthologues as those genes present in a single copy in all species being ...
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