The rumen is a complex ecosystem composed of anaerobic bacteria, protozoa, fungi,
methanogenic archaea and phages. These microbes interact closely to breakdown plant material …

Functional partnerships between proteins are at the core of complex cellular phenotypes,
and the networks formed by interacting proteins provide researchers with crucial scaffolds for …

We have developed an automatable procedure for reconstructing the tree of life with branch
lengths comparable across all three domains. The tree has its basis in a concatenation of 31 …

Background In recent years, model based approaches such as maximum likelihood have
become the methods of choice for constructing phylogenies. A number of authors have shown …

With the increasing availability of various ‘omics data, high-quality orthology assignment is
crucial for evolutionary and functional genomics studies. We here present the fourth version …

Software for visualizing sequence alignments and trees are essential tools for life scientists.
In this review, we describe the major features and capabilities of a selection of stand-alone …

Productivity of ruminant livestock depends on the rumen microbiota, which ferment indigestible
plant polysaccharides into nutrients used for growth. Understanding the functions carried …

Horizontal gene transfer, in which genetic material is transferred from the genome of one
organism to that of another, has been investigated in microbial species mainly through …

The goal of the H ungate1000 project is to generate a reference set of rumen microbial
genome sequences. Toward this goal we have carried out a meta‐analysis using information …

… CJ Creevey … CJ Creevey, JO McInerney, Clann: investigating phylogenetic information
through … Supplementary information: Clann has been written in the C programming language. …