I want to draw a phylogenetic tree of 1000 bacterial species, so that I can use that tree in phylogenetic independence method such as PIC or PGLS. But I am afraid if I ll draw tree by myself using 16S or any other marker , may be it will not be that much reliable. So, can anybody suggest me any site or database from where I can download the full bacterial or prokaryotic tree in NEXUS format.
For bacteria, I think you will really need to consider which 1,000 species you choose. The eubacteria and archaebacteria have both been evolving for a lot longer than the eukaryotes which are a hybrid or fusion of bacteria (the mitochondria, chloroplasts and a few of the nuclear genes) and archaebacteria (which apparently contributed mostly to the nuclear genes of eukaryotes (plants, animals, fungi, protists). PIC and PGLS analysis are based on phylogenetic distance measurements, which are nonlinear over those types of time scales. Phylogenetic distances can be quite linear over timescales of zero to 100 million years or so in bacterial evolution (or mitochondrial or chloroplast genomes) but over billions of years it gets very messy. Studying 1000 species of enterobacteria or 1000 species of Escherichia might be better than trying to compare enterobacteria to clostridia and other very diverse bacteria.
https://academic.oup.com/sysbio/article/61/3/382/1669127
I love this one: https://www.nature.com/articles/nmicrobiol201648#s6 Newick file in supplement. Although I don't know if it is robust enough to include as a reference phylogeny.
Here another interesting database https://www.arb-silva.de/projects/living-tree/
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