davidemms/OrthoFinder issues and pull requests

#931 - How accurate can be Orthofinder using small proteomes files?

Issue - State: closed - Opened by MauriAndresMU1313 3 months ago - 1 comment

#930 - Using scripts to process protein data from NCBI

Issue - State: open - Opened by wang748 3 months ago - 8 comments

#929 - ASTRAL-Pro need GLIBC_2.** when using OrthoFinder 3.0.1b1

Issue - State: closed - Opened by BioOmics 3 months ago - 1 comment

#928 - ModuleNotFoundError: No module named 'scripts_of'

Issue - State: open - Opened by caonetto 3 months ago - 1 comment

#927 - Conda environment diamond version is super old (0.9.10)?

Issue - State: closed - Opened by shjenkins94 3 months ago - 2 comments

#926 - Only 1 gene in HOG in N0.tsv

Issue - State: open - Opened by sunriseTM 4 months ago - 6 comments

#925 - -X option

Issue - State: open - Opened by H1889 4 months ago

#924 - PermissionError: [Errno 1] Operation not permitted

Issue - State: closed - Opened by Ming314 4 months ago - 1 comment

#923 - Running with pre-blast results gets stuck

Issue - State: closed - Opened by yyliang12 5 months ago - 1 comment

#922 - Question_outputs_Pangenome

Issue - State: closed - Opened by cristoyerenahs 5 months ago - 5 comments

#921 - Inferring remaining multiple sequence alignments and gene trees——This step has been stuck for ten days

Issue - State: open - Opened by YuJiang0121 5 months ago - 4 comments

#920 - disagreement between OrthologuesStats_one-to-one.tsv and Orthogroups.GeneCount.tsv

Issue - State: open - Opened by shiyi-pan 6 months ago - 8 comments

#919 - Running OrthoFinder with Large Species Set (>2k)

Issue - State: open - Opened by BioOmics 6 months ago - 9 comments

#918 - Option to stop Orthofinder after building the species tree?

Issue - State: closed - Opened by Laura-Alex 6 months ago - 2 comments

#917 - Diamond stuck on "Running diamond all-versus-all"

Issue - State: closed - Opened by zoemullersnakes 6 months ago - 1 comment

#916 - header changed in MSA

Issue - State: closed - Opened by jpinus 6 months ago - 1 comment

#915 - Option to start Orthofinder at stage of inferring trees from MSAs?

Issue - State: open - Opened by PollyHannah 6 months ago - 1 comment

#914 - About -a option: using pre-computed BLAST results does not increase the number of orthofinder threads

Issue - State: closed - Opened by goshng 6 months ago - 1 comment

#913 - HIV teste 1

Issue - State: closed - Opened by Dribio1 6 months ago - 4 comments

#912 - issue with running Orthofinder

Issue - State: closed - Opened by SrichandanPadhi 7 months ago - 2 comments

#911 - Question_process_Orthofinder

Issue - State: closed - Opened by cristoyerenahs 7 months ago - 2 comments

#910 - what is the Orthogroup column in N*.tsv?

Issue - State: closed - Opened by aguang 7 months ago - 1 comment

#909 - not an issue, clarification wanted for which sequences are represented in orthogroups

Issue - State: closed - Opened by vmkhot 7 months ago - 4 comments

#908 - Single copy orthologs (SCO) are not being generated

Issue - State: closed - Opened by timurrxxcd 7 months ago - 1 comment

#907 - [Feature Request] Allow for passing options to Diamond and other dependencies

Issue - State: closed - Opened by StefanFlaumberg 7 months ago - 1 comment

#906 - [Possible Bug] The `-og` option doesn't stop after inferring orthogroups

Issue - State: open - Opened by StefanFlaumberg 7 months ago - 1 comment

#905 - Species tree make_ultrameric.py not working

Issue - State: closed - Opened by aebaci 7 months ago - 1 comment

#904 - total identical sequences clustered into one orthogroup, but the topology of gene tree divided into multiple clades

Issue - State: closed - Opened by liping-jiang 8 months ago - 1 comment

#903 - 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.

Issue - State: open - Opened by timurrxxcd 8 months ago - 3 comments

#902 - "Invalid escape sequence" errors while starting OrthoFinder

Issue - State: open - Opened by markusHaferkamp 8 months ago - 2 comments

#901 - Duplicates of the same gene in Orthogroup sequence files

Issue - State: closed - Opened by niconps14 8 months ago - 3 comments

#900 - -T raxml-ng——ERROR: Species tree inference failed

Issue - State: open - Opened by suncimu 8 months ago - 5 comments

#899 - Issue with rerunning orthofinder "from trees" step -- Blast0_0.txt not found

Issue - State: open - Opened by 00-kelvin 8 months ago - 4 comments

#898 - Which directories for versions of Orthofinder v2.4.0 (or more recent) are valid with the HOGs?

Issue - State: open - Opened by SheepwormJM 8 months ago

#897 - Inferring gene trees with for orthogroups with less than 4 sequences

Issue - State: closed - Opened by niconps14 8 months ago - 1 comment

#896 - ERROR: external program called by OrthoFinder returned an error code: -9

Issue - State: open - Opened by zishanw 9 months ago

#895 - ValueError: setting an array element with a sequence.

Issue - State: open - Opened by gsierrar 9 months ago

#894 - Identifying number of characters involved in species tree inference using -M msa option

Issue - State: open - Opened by Fatma116 9 months ago

#893 - is it possible to specify a tree for orthofinder?

Issue - State: open - Opened by AlexGalvez 9 months ago - 1 comment

#892 - Get order of concatenated sequences in SpeciesTreeAlignment.fa

Issue - State: open - Opened by SalvadorGJ 9 months ago

#891 - Orthogroups vs Superfamily Family Tree

Issue - State: open - Opened by 000generic 9 months ago

#890 - OSError: [Errno 24] Too many open files [32514] Failed to execute script 'orthofinder' due to unhandled exception!

Issue - State: open - Opened by MassimoCasagranda 10 months ago

#889 - Add kalign support

Pull Request - State: closed - Opened by photocyte 10 months ago - 1 comment

#888 - DockerFile

Issue - State: open - Opened by TheLillo 10 months ago

#887 - Only two species comparison, but the number of one-to-one orthologs in Orthologues Stats one_to_one.tsv is more than the number of single-copy orthogroups in statistics Overall.tsv file

Issue - State: open - Opened by HyCipher 10 months ago

#886 - Is it possible to detect Orthologous Isoforms

Issue - State: open - Opened by Tang-pro 10 months ago

#885 - Rooted species tree branch length meaning

Issue - State: open - Opened by jmpolinski 11 months ago - 1 comment

#884 - ERROR when starting from BLAST, Orthogroups or Tree

Issue - State: open - Opened by geboro 11 months ago

#883 - [Feature request] reduce number generated files per directory (e.g. for blast results, pickle files)

Issue - State: open - Opened by mpice-mn 11 months ago

#882 - [Bug:] Option `-p tmp_pickle_dir` not working

Issue - State: open - Opened by mpice-mn 11 months ago

#881 - conda install failes

Issue - State: open - Opened by shbrainard 11 months ago - 1 comment

#880 - Added conda installation

Pull Request - State: open - Opened by dadrasarmin 11 months ago

#879 - Issue with user supplied species tree

Issue - State: open - Opened by mollylRivers 11 months ago

#878 - Installing on Mac M1 - README update

Issue - State: open - Opened by Neato-Nick 11 months ago

#877 - Update README.md

Pull Request - State: closed - Opened by dadrasarmin 11 months ago

#876 - different sets of genes as input

Issue - State: open - Opened by NilsHassel 11 months ago

#875 - paralogs in same species

Issue - State: open - Opened by NilsHassel 11 months ago

#874 - To run STAG/STRIDE without requiring all species present in tree/ output with only species present in all trees

Issue - State: closed - Opened by tsa4a12 about 1 year ago - 1 comment

#873 - diamond dropped --ignore-warnings flag, leads to error

Issue - State: closed - Opened by ryan-preble about 1 year ago - 5 comments

#872 - ERROR: .fas appears to contain nucleotide sequences instead of amino acid sequences. Use '-d' option

Issue - State: closed - Opened by xiongqian123456789 about 1 year ago

#871 - -M msa -T raxml fails in OrthoFinder 2.5.5

Issue - State: open - Opened by wpfeiffer about 1 year ago - 1 comment

#870 - Orthofinder not writing gene to HOG even though it matches all others in the group

Issue - State: open - Opened by A-Swafford about 1 year ago

#869 - Running with GLIBC 2.17

Issue - State: closed - Opened by evaaagkat about 1 year ago

#868 - An error is reported when running orthofinder for more than 15 species

Issue - State: open - Opened by MYP0130 about 1 year ago

#867 - Pan Plot as Roary

Issue - State: open - Opened by MdUmar-tech about 1 year ago

#866 - From Orthogroups to a core Proteome

Issue - State: open - Opened by Saeedjaanz about 1 year ago

#865 - Broken link to tutorials in README

Issue - State: open - Opened by ElizabethBrooks about 1 year ago

#864 - Orthogroups.txt and Orthogroups.csv files do not match

Issue - State: open - Opened by glmaala about 1 year ago - 1 comment

#863 - Orthologic Subfamily identification

Issue - State: open - Opened by kittyBS about 1 year ago

#862 - adding and removing proteomes - all-vs-all blast

Issue - State: open - Opened by ArtemPankin about 1 year ago

#861 - 生信分析求助，报错137，ERROR: external program called by OrthoFinder returned an error code: 137

Issue - State: open - Opened by Statistic-Qin over 1 year ago - 4 comments

#854 - orthofinder出现too many values to unpack 怎么解决

Issue - State: open - Opened by whz236 over 1 year ago - 3 comments

#852 - manually running "remaining multiple sequence alignments and gene trees"

Issue - State: open - Opened by chklopp over 1 year ago - 1 comment

#846 - Non-default output directory should be used with -b

Issue - State: open - Opened by SalvadorGJ over 1 year ago - 2 comments

#845 - some genes lost in OrthoGroup when running orthofinder with additional species

Issue - State: open - Opened by leon945945 over 1 year ago

#844 - Ubuntu 20.04 error ('GLIBC_2.35' not found)

Issue - State: closed - Opened by sz-1002 over 1 year ago - 1 comment

#843 - The problem of gene miss in clustering

Issue - State: open - Opened by Aure712 over 1 year ago

#842 - Problem with running OrthoFinder after custom diamond search with modified e-value thresholds

Issue - State: open - Opened by JaJeBacz over 1 year ago

#841 - copy number change after adding new species

Issue - State: open - Opened by AlisaGU over 1 year ago

#840 - ERROR: Species tree inference failed

Issue - State: open - Opened by SHMinger over 1 year ago - 3 comments

#839 - error : UnboundLocalError: cannot access local variable 'speciesTree' where it is not associated with a value

Issue - State: open - Opened by yogurtYH over 1 year ago

#838 - orthofinder diamond multi-threading issues with large files

Issue - State: open - Opened by HweeSze over 1 year ago

#837 - About MultipleSequenceAlignments SpeciesTreeAlignment.fa file

Issue - State: open - Opened by ClarenceHsiang over 1 year ago

#836 - How to understand "species-specific orthogroups"?

Issue - State: open - Opened by xiekunwhy over 1 year ago

#835 - Error: Species tree inference failed

Issue - State: open - Opened by emdtr over 1 year ago - 4 comments

#834 - Using Nucleotide vs Amino Acid fastas as input

Issue - State: open - Opened by liamfriar over 1 year ago - 1 comment

#833 - accidental extra node

Issue - State: closed - Opened by Rhia15 over 1 year ago

#832 - difference between nucleotide and amino acid sequences

Issue - State: closed - Opened by Rhia15 over 1 year ago - 2 comments

#831 - Error when Inferring remaining multiple sequence alignments and gene trees

Issue - State: open - Opened by marcodimarsico over 1 year ago - 1 comment

#830 - Cannot run BLAST+ (using docker on Windows)

Issue - State: closed - Opened by fajardogomez over 1 year ago - 3 comments

#829 - Are there any Bootstrap values on the node of gene tree in Resolved Gene Trees Directory?

Issue - State: closed - Opened by xbx-xbx-1208 over 1 year ago - 1 comment

#828 - Full reconciliation results in the output

Issue - State: open - Opened by ens-sb over 1 year ago

#827 - OrthoXML output issues

Issue - State: open - Opened by ens-sb over 1 year ago

#826 - Cannot run diamond v 2.5.5

Issue - State: closed - Opened by isokoten over 1 year ago - 4 comments

#825 - diamond potential incompatability

Issue - State: closed - Opened by nhartwic over 1 year ago - 1 comment

#824 - Meaning of branch lengths in resolved gene trees

Issue - State: closed - Opened by JasonAnthonyHill over 1 year ago - 3 comments

GitHub / davidemms/OrthoFinder issues and pull requests