Questions tagged [orthofinder]
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9
questions
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votes
2
answers
44
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Error with eggNOG-mapper jobs
I recently tried using eggNOG-mapper for pan-genome and core genome analysis of files from OrthoFinder, specifically the 'Orthogroup_Sequences' which contains a huge list of protein files in fasta ...
- 105
1
vote
1
answer
139
views
How to add bootstrap values to the phylogenetic tree generated by OrthoFinder?
When we run the OrthoFinder analysis tool on a group of genomes to get the orthologues shared by them one of the output files include a folder named 'Species_Tree' that contains a text file named '...
- 105
1
vote
1
answer
83
views
How to use Gblocks for trimming single-copy gene sequences?
I have run OrthoFinder on a set of 11 genomes and got the results in a folder. From the output folder, I saved all the single-copy gene sequences in a single FASTA file and now wish to remove all gaps ...
- 105
1
vote
1
answer
46
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Given a FASTA file with a set of genes, how do I determine that set's conservation among a genetic order?
Given a set of genes in a FASTA-formatted file, for example: exFasta.fa, what is the best way to determine how well conserved the genes in that file are among an ...
- 11
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votes
2
answers
58
views
expansions and contractions from OrthoFinder
The input file looks like this, and the complete file can be found here:
...
- 275
3
votes
1
answer
353
views
How to analyse Orthofinder results
I read this paper (Colletotrichum shisoi sp. nov., an anthracnose pathogen of Perilla frutescens in Japan: molecular phylogenetic, morphological and genomic evidence). We ran Orthofinder and also ...
- 275
2
votes
1
answer
204
views
No bootstrap value on single-copy gene tree created by OrthoFinder
I'm running analysis with OrthoFinder and it produces a single-copy gene tree. When I visualize the tree with iTOL, there's no bootstrap value on the branches or nodes. There's a published paper in ...
- 51
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vote
1
answer
112
views
Number of sing-copy genes identified by orthofinder is far less than BUSCO assessment?
Dear Orthofinder users and BUSCO users,
Recently, I have assessed 30 genome annotataions using BUSCO with lineage dataset ...
- 81
0
votes
1
answer
60
views
Removing data from OrthoFinder output prefix
I am using OrthoFinder to find orthogroups between species. I am using the latest version unpacked through tar as per their instructions.
Orthofinder creates an output folder according to the current ...
