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Hi,
I'm try to run a first test with my own data. It's about 3 very closely related genomes, already aligned with Cactus. I'm preparing the configuration file following the instruction. I have a bu…
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Hello! I have a question about scaling trait variables. I have a model where it seems that I need to rescale my trait variables before sampling to avoid an error. This was unexpected because I know HM…
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One large limitation with the rooted datasets is that they are all outgroup rooted. This does not conform to the more general case where the root could be anywhere, and it is important to see how vari…
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Hello,
I am annotating a lot of new chlorophyta genomes from an order that is distantly related to anything sequenced. Many don't have RNA data, so I am aligning RNA with the closest related speci…
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For discussion surrounding the best ways to make comparisons between this and other supertree methods.
The current method I have set up for birth death trees is to generate a model birth death tree…
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Hi,
I am having problems similar to issue #690 related to building a phylogenetic tree.
Housekeeping first:
```bash
Anvi'o version ...............................: margaret (v5.1)
Profile D…
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### Active Development
Yes
### Tool name
phylosem
### Tool abbreviation
phylosem
### Author(s)
James Thorson and Wouter van der Bijl
### NOAA Internal
Yes
### Maintainer Name
James Thorson
…
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See https://github.com/JuliaGraphs/LightGraphs.jl/blob/master/CONTRIBUTING.md - this is rendering as http://juliagraphs.github.io/LightGraphs.jl/latest/contributing/ - and if you scroll down to the "D…
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I used 40,000 influenza HA nucleotide sequences with a sequence length of 987. Maple gave me a warning that there are sequences divergence exceeding 0.1. The final output tree has tens of thousands of…
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Hi, I'm trying to run saturation test for mitochondrial 16S rRNA gene partial sequence with total 291 positions and 300 sequences.
When I try to run saturation test (I tried almost all available opt…