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Hi, I have a phyloseq object containing a phylogenetic tree at OTU level and I would like to do somenthing like this:
data(GlobalPatterns)
GP 0, GlobalPatterns)
GP.chl
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I am trying to add a geom_hilight layer to identify two clades in a phylogeny. The tree is then aligned to a heatmap with cowplot. The alignment works well without the geom_hilight, but once it has be…
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Branch lengths must reflect distances between clades as read in from newick.js.
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Given that the definition of monophyletic groups relies on named clades anyway, it would make sense to specify the required monophyly restrictions not only through monophyly levers, but optionally als…
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We will typically just need to get clade assignments (and summarize to counts of clade assignments) for samples that were collected within a particular date range. We should be able to specify those …
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Node index of MRCA of clades may change during MCMC, but FLC's implementation assumes the node number of the MRCA of a clade does not change. This needs to be fixed for relaxed clock FLC analyses.
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I just realised, we might well want to be able to harvest vernaculars (but definitely not images) for entire clades, e.g. Platyrrhini-> "New World Monkeys". We could either expand the remit of the `ge…
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Hi there,
I'm trying to visualize a tree with multiple selected clades being scaled (condensed) and collapsed to save space for a publication figure.
I've seen the issue also reported in the [gg…
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- Consistently update set of reference transcripts for library source inference and include more genes for better accuracy
- Include organisms/sources from all clades in Ensembl: Bacteria, Plants, Fu…
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Hello,
Thank you for this amazing phylotree.js library, it allows you to customize so many things. After researching a few libraries, I settled on this one to visualize a phylogenetic tree.
I am…