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Dear Treeshrink,
I have a loci.treefile with about 3800 gene trees. An issue arises due to gene trees with "too many taxa" when really, the genes are split in their alignment files due to poor seq…
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Hi,
thanks a lot for providing this excellent software, very useful!
I’d have a few questions about the core_gene_sweeps module. Hope it’s ok that I put them together in one issue here.
**1) Em…
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Hi, liang:
After done the simulation of gene trees using Phybase, i want do a correlation analyses between simulated genetrees and empirical gene trees , like this:
![图片](https://user-images.githubu…
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Hi Simon,
I am currently using Twisst (which seems like a fantastic program!) to look at the weighted topologies of trees across chromosomes in my study group. Including an outgroup, there are ~6-8…
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Hello,
I'm trying to run a RERconverge analysis on a set of gene trees from non-model organisms that were derived from a tree-based ortolog extraction algorithm, so most gene trees do not have all th…
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Hello,
I'm trying to run SODA program on my dataset. I have a set of gene trees in a single file called loci.treefile. I get following error when I run it
Traceback (most recent call last):
Fil…
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Assume that if a gene file exists, that gene tree has been produced. Therefore start from the remaining trees.
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Hi! Thanks for the great package, I use parts of it routinely without issue.
I have a question about how to interpret the NAs sometimes outputted in boot.phylo() after using nj(dist(data_matrix)) …
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Hi @wadedismukes @jjustison ,
I've been using treeducken for teaching a phylogenetic course, in which the students will generate a bunch of gene trees under a specific species tree. However, I found …
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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…