2019年12月2日 · Here we build a reference phylogeny of 10,575 evenly-sampled bacterial and archaeal genomes, based on a comprehensive set of 381 markers, using multiple strategies. Our trees indicate...

In this study, we aimed to perform genome-wide comparisons of different bacterial species, namely Escherichia coli, Shigella, Yersinia, Klebsiella, and Neisseria spp., based on their K-mer profiles to construct phylogenetic trees.

2023年4月20日 · In this study, we aimed to perform genome-wide comparisons of different bacterial species, namely Escherichia coli, Shigella, Yersinia, Klebsiella, and Neisseria spp., based on their K-mer profiles to construct phylogenetic trees.

2021年5月7日 · A rooted bacterial tree is necessary to understand early evolution, but the position of the root is contested. Here, we model the evolution of 11,272 gene families to identify the root, extent of horizontal gene transfer (HGT), and the nature …

2016年4月11日 · Here, we use new genomic data from over 1,000 uncultivated and little known organisms, together with published sequences, to infer a dramatically expanded version of the tree of life, with...

2018年8月27日 · Here we present a phylogeny inferred from the concatenation of 120 ubiquitous single-copy proteins, and we used this phylogeny to propose a bacterial taxonomy that covers 94,759 bacterial...

We present a systematic approach for constructing a phylogenetic tree based on simultaneously clustering the complete proteomes of 360 bacterial species. From the homologous clusters, we identify 49 protein sequences shared by 99% of the organisms to build a tree.

2013年4月25日 · Here, we employ several phylogenetic methods to infer the phylogeny of the bacteria and archaea for which genome sequences are available, using a set of 24 single-copy, ubiquitous genes (Table 1).

2017年10月17日 · Bypassing the need for genome availability, we present a snapshot of bacterial phylogenetic diversity based on the recovery of high-quality SSU rRNA gene sequences extracted from nearly 7000 metagenomes and all available reference genomes.

2024年8月29日 · It uses the amino acid and nucleotide sequences from a defined number of the BV-BRC Global Protein Families (PGFams) [2], which are picked randomly, to build an alignment, and then generate a tree based on the differences within those selected sequences.