Are there any open-source tools that can take a list of species and generate newicks for them (time agnostic is more than fine).
I found CRAN atpg but turns out it is deprecated and does not install for latest version of R. Got it installed on a compatable version of R but it runs without output I say open-source for the sake of accessibility for downstream peer-reviewers.
I also found CRAN phybase, also heavily deprecated with.
I found phyloT which does exactly what I want and does say that its information is sourced from NCBI but is a paid subscription based tool. (which is perhaps not ideal for downstream peer-review).
There is NCBI taxonom common-tree but it does not generate Newicks.
I need to generate a newick file for a north of a hundred species and make various subsets so making many of them by hand is probably not the best way to go about this, I think a decent alternative would be to have one large newick file and have something like ggtree subset the main newick file. This would save a lot of time in general but I cannot quite pin down the ggtree syntax to filter a larger newick against a sub-list of species names. Aesthetic sub-setting seems to be a discussed idea but I cannot find phylogenetic sub-setting. Do you guys have any ideas?
Sorry, I think the way I phrased it was not clear enough. I am familiar with IQtree, it generates gene-trees for multiple sequence aligned files and I don't think it can take a list of taxa as input to generate specie newicks. Thanks though! I think I will have to draw my newick trees by hand.