Questions tagged [orthofinder]

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2 votes
2 answers
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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 ...
K_081's user avatar
  • 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 '...
K_081's user avatar
  • 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 ...
K_081's user avatar
  • 105
1 vote
1 answer
46 views

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 ...
Jacob's user avatar
  • 11
2 votes
2 answers
58 views

expansions and contractions from OrthoFinder

The input file looks like this, and the complete file can be found here: ...
user3523406's user avatar
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 ...
user3523406's user avatar
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 ...
raysteven's user avatar
1 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 ...
YP CHEN's user avatar
  • 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 ...
Michael Winter's user avatar