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Hi,
I`ve just got this error while running Orthofinder 2.5.4 (-M msa -t 64 -a 8) in a CentOS cluster. It seems the analysis is still going on, but should I be worried? Any idea about what may have ca…
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Hi,
I am going to be using CSUBST in an exploratory manner on a number of genes from a phylogeny and I have both a species tree and gene trees (for each gene) available to me. Can you recommend the…
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In many of my Orthogroup sequence files, within the same orthogroup I am getting duplicate copies of the same exact gene, with identical identifiers and amino acid sequences. My original fasta files t…
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Hi Simon,
I'm interested in using TWISST to test a few hypotheses about support for different lineage relationships. My samples can be assigned to 12 lineages (including an outgroup) but not all l…
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Dear Developers,
I used IQ-TREE to construct gene trees for individual loci, with a total of 8276 loci. However, only 8229 were successfully constructed. I checked one example of the unsuccessful cas…
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Hello,
How do I interpret the fact that ASTRAL is reporting a normalized quarter score greater than 1? Here is some of the output from the log:
```
Using polytree-based weight calculation.
Numb…
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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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I would like to compare both plastome and nuclear trees using the same set of data. However, assembling all the gene loci for both has been challenging especially for chloroplast loci. I generated a t…
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Hi ,
I am new to this field and I am currently working on my master's thesis, focusing on the evolution of a specific morphological trait., I've opted to analyze 60 genes across a smaller number of…
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Good afternoon,
I am having trouble running MP-EST v 3.0 both on my institution's linux cluster and on the research group's mac. Both times I am able to run the test dataset without any issues. It…