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It is my genome.repeat.stats results:
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total 169152450 bp sites were identified to be repeat
DNA:
CMC-EnSpm 10728 11492609
IS3EU 9 10560
MULE-MuDR …
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hello @oushujun
I noticed that ".superfam.size.list "has a large proportion of" unkonwn "items, I am surprised by this "unknown" definition; Are they LTR retrotransposons or some other unknown pi…
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Hi,shujun,
Today i use ltr_finder to create CIDE.scn : ltr_finder -w 2 -C -D 15000 -d 1000 -L 7000 -l 100 -p 20 -M 0.85 CIDE.fa >CIDEscn .
And then run LTR_retriever -genome CIDE.fa -infinder C…
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Hello, @zhangrengang
I am studying how to extract the CDS sequence of all LTR, but I don't know how to do it. Reference from: https://onlinelibrary.wiley.com/doi/10.1111/jse.12850. But the above…
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Hi,
I am working on a genome comparison between two plant species, currently focusing on a number of genes that have been unable to be assigned to an Orthogroup. I initially interpreted 'Unassigned…
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Hello,@[thomaskf](https://github.com/thomaskf)
Iqtree2 was used to build evolutionary trees but it was found to take too long. It's been more than ten days. I constructed an evolutionary tree of RT…
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Hello @oushujun
I used the LTR-retriever to extract the transposon of a species, assuming a GFF file named 1.fna.mod.ltr.homo.gff3 was generated. Assume that the genome GFF file of the species is GC…
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Hi, I've had some really interesting results from EDTA, thank you for your work on this program. I have a question about the nested TE analysis performed by EDTA: I have looked at the files ".stat.all…
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Hi dear developers,
Many thanks for your excellent tools! I have some questions.
1. I noticed the outputs in the path labeled with *raw and *intact. Looking into the scripts, the *LTR.raw.fa seemed …
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Hello,owner!
As mentioned,when the softeare run to the “Creating fast initial parsimony tree by random order stepwise addition...” step,it just stoped. Notthing happened then. No any information …