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Following your Q&A I am trying to use Weighted ASTRAL - Hybrid (i.e. astral-hybrid) with the bootstrap gathered for my 3000 gene trees.
> Q: I have gene trees with branch lengths and Bootstrap/Bays…
drelo updated
2 weeks ago
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The "Inferring remaining multiple sequence alignments and gene trees" has been ended by our SLURM scheduler due to time limit. Only 6 jobs out of 35000 were still running. Is it possible to run them m…
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I'm interested in visualizing gene tree distributions over taxa with a high rate of gene gain and loss. So, the set of tips in each of the gene trees is not the same. In principle, it should be possib…
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Dear Developers,
I just realized, that the README supplied with the 1KP example data, states that gene trees need to be rooted. In the main README, I could not find any information about rooting ge…
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Hi,
I'm using ASTRAL tool to get the species tree using gene trees. I have created the gene trees and the bootstrap gene trees using RAxML. This is the code I have used in ASTRAL.
java -jar Astral/a…
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Hi,
I'm currently using SimPhy to simulate gene trees off of a provided species tree and a data frame with simulation parameters. The data frame I provide is 2000 lines long, and I expect to recei…
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Thank you for the tutorial. The GBE paper was extremely informative and greatly enhanced my understanding of reconciliation processes.
I am wondering if a single gene tree can be used for reconcil…
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Include no of SNPs used to build SNP tree and no of genes used to build core gene phylogeny.
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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,
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…