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Hello,
I apologize if a similar issue has been posted elsewhere, but I did not find one when I searched.
I am trying to annotate a new reference genome (a marine fish; assembly is near-chromosom…
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Hello,
weightMat
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Hello again,
I am running 90 days now Orthofinder for 30 species. Yesterday my job killed in the gene constuction step (raxm-ng).
So, is there any solution to rerun orthofinder again from this st…
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Our cluster has a new policy of allowing only a million files per user, and I'm feeling this limit with a few Orthofinder runs - there are tens of thousands of files in the Orthogroup_Sequences, Resol…
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Hello,
I am trying to run the Twisst with my set of gene trees (3963), created with IQTree (newick format). I have created these trees with 84 individuals belonging to 8 different groups. And for so…
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When the mapping file is inconsistent with the guide tree, the error is not clear:
~~~bash
(base) bash-3.2$ python run_delimitation.py -i sample_data/all-gene-trees.tre.pruned -o lizards-speciatio…
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Hi,
I successfully run orthofinder using the protein sequences, but I get an error when I run it again using the nucleotide sequences from the same species.
I have DNA sequences for 71 species. Th…
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Does your program output all of the IBD segments? I am curious about the parameter. Is this parameter designed to manage memory and runtime resources? Could using too small of a value for this parame…
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Hi,
I'm trying to use treespace for the comparison of individual gene phylogenies to overall "species" phylogenies. Most of my data is from single-cell sequencing, which means individual genomes an…
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**The issue**: When there are many gene trees, phyparts takes very long time to finish. However, by splitting the gene trees into smaller subsets, phyparts is much quicker.
**The idea**: Would it …