davidemms OrthoFinder issues

davidemms / OrthoFinder

Phylogenetic orthology inference for comparative genomics

https://davidemms.github.io/

GNU General Public License v3.0

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issues

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Extract edge weights from graph file

#945 gauravdiwan89 opened 2 days ago
5
Gene in many orthogroups

#944 EmilyPhelps opened 3 days ago
1
Are there HOG alignments and gene trees in OrthoFinder output?

#943 000generic opened 3 days ago
2
More species with lower quality genomes finishes faster

#942 000generic opened 5 days ago
2
issues with results post "--assign", single gene in multiple Orthogroups

#941 nhartwic opened 1 week ago
3
error mcl -9 no such file "clusters_OrthoFinder_I1.5.txt"

#940 cpouchon opened 1 week ago
5
User-specified species tree with core/assign workflow

#939 SalvadorGJ opened 1 week ago
3
ERROR: Query or hit sequence ID in BLAST results file missing or incorrectly formatted

#938 jrdred opened 1 week ago
1
orthofinder3 "assign" option failed

#937 uguyet opened 1 week ago
3
Failing and hanging after gene tree inference

#936 KyleTDavid closed 1 week ago
1
Sequence IDs in single copy orthologs from RefSeq cds data

#935 marctollis opened 2 weeks ago
1
Importing Custom Rooted Gene Trees into OrthoFinder for DLC Analysis

#934 Li-Yuanshuo opened 2 weeks ago
1
User-specified rooted species tree

#933 dahaigui opened 2 weeks ago
1
Test can run "muscle" - failed

#932 dongyiyi opened 3 weeks ago
2
How accurate can be Orthofinder using small proteomes files?

#931 MauriAndresMU1313 closed 1 month ago
1
Using scripts to process protein data from NCBI

#930 wang748 opened 1 month ago
12
ASTRAL-Pro need GLIBC_2.** when using OrthoFinder 3.0.1b1

#929 BioOmics closed 1 month ago
1
ModuleNotFoundError: No module named 'scripts_of'

#928 caonetto opened 1 month ago
1
Conda environment diamond version is super old (0.9.10)?

#927 shjenkins94 closed 1 month ago
2
Only 1 gene in HOG in N0.tsv

#926 sunriseTM opened 1 month ago
6
-X option

#925 H1889 opened 1 month ago
0
PermissionError: [Errno 1] Operation not permitted

#924 Ming314 closed 1 month ago
1
Running with pre-blast results gets stuck

#923 yyliang12 closed 1 month ago
1
Question_outputs_Pangenome

#922 cristoyerenahs closed 1 month ago
5
Inferring remaining multiple sequence alignments and gene trees——This step has been stuck for ten days

#921 YuJiang0121 opened 3 months ago
4
disagreement between OrthologuesStats_one-to-one.tsv and Orthogroups.GeneCount.tsv

#920 shiyi-pan opened 3 months ago
8
Running OrthoFinder with Large Species Set (>2k)

#919 BioOmics closed 1 week ago
9
Option to stop Orthofinder after building the species tree?

#918 Laura-Alex closed 3 months ago
2
Diamond stuck on "Running diamond all-versus-all"

#917 zoemullersnakes closed 1 month ago
1
header changed in MSA

#916 jpinus closed 1 month ago
1
Option to start Orthofinder at stage of inferring trees from MSAs?

#915 PollyHannah opened 4 months ago
1
About -a option: using pre-computed BLAST results does not increase the number of orthofinder threads

#914 goshng closed 3 months ago
1
HIV teste 1

#913 Dribio1 closed 3 months ago
4
issue with running Orthofinder

#912 SrichandanPadhi closed 3 months ago
2
Question_process_Orthofinder

#911 cristoyerenahs closed 3 months ago
2
what is the Orthogroup column in N*.tsv?

#910 aguang closed 3 months ago
1
not an issue, clarification wanted for which sequences are represented in orthogroups

#909 vmkhot closed 4 months ago
4
Single copy orthologs (SCO) are not being generated

#908 timurrxxcd closed 3 months ago
1
[Feature Request] Allow for passing options to Diamond and other dependencies

#907 StefanFlaumberg closed 3 months ago
1
[Possible Bug] The `-og` option doesn't stop after inferring orthogroups

#906 StefanFlaumberg opened 5 months ago
1
Species tree make_ultrameric.py not working

#905 aebaci closed 3 months ago
1
total identical sequences clustered into one orthogroup, but the topology of gene tree divided into multiple clades

#904 liping-jiang closed 3 months ago
1
Hello! I have 11 .faa files in a folder. I ran orthofinder -d -f /public/home/newfasta -t 64 -o output_orthofinder. But after 13-14 minutes process failed. There is no error. I opened slurm.out file then checked. there was written like below.

#903 timurrxxcd opened 5 months ago
3
"Invalid escape sequence" errors while starting OrthoFinder

#902 markusHaferkamp opened 5 months ago
2
Duplicates of the same gene in Orthogroup sequence files

#901 niconps14 closed 3 months ago
3
-T raxml-ng——ERROR: Species tree inference failed

#900 suncimu opened 6 months ago
5
Issue with rerunning orthofinder "from trees" step -- Blast0_0.txt not found

#899 00-kelvin opened 6 months ago
4
Which directories for versions of Orthofinder v2.4.0 (or more recent) are valid with the HOGs?

#898 SheepwormJM opened 6 months ago
0
Inferring gene trees with for orthogroups with less than 4 sequences

#897 niconps14 closed 6 months ago
1
ERROR: external program called by OrthoFinder returned an error code: -9

#896 zishanw opened 6 months ago
0