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Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences
TLDR
The results demonstrate that phylogeny and function are sufficiently linked that this 'predictive metagenomic' approach should provide useful insights into the thousands of uncultivated microbial communities for which only marker gene surveys are currently available.
STAMP: statistical analysis of taxonomic and functional profiles
TLDR
UNLABELLED STAMP is a graphical software package that provides statistical hypothesis tests and exploratory plots for analysing taxonomic and functional profiles and a user-friendly graphical interface permits easy exploration of statistical results and generation of publication-quality plots.
Identifying biologically relevant differences between metagenomic communities
TLDR
Examination of a pair of iron mine metagenomes demonstrates that deeper biological insights can be gained using statistical techniques available in the new software package, STAMP, that supports best practices in analysis and reporting.
CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database
TLDR
A new Resistomes & Variants module provides analysis and statistical summary of in silico predicted resistance variants from 82 pathogens and over 100 000 genomes, able to summarize predicted resistance using the information included in CARD, identify trends in AMR mobility and determine previously undescribed and novel resistance variants.
Highways of gene sharing in prokaryotes.
TLDR
A rigorous phylogenetic analysis of >220,000 proteins from genomes of 144 prokaryotes suggests a pattern of inheritance that is largely vertical, but with notable exceptions among closely related taxa and among distantly related organisms that live in similar environments.
Phylogenetic identification of lateral genetic transfer events
TLDR
The high degree of consistency among inferred protein trees shows that vertical inheritance is the dominant pattern of evolution, at least for the set of organisms considered here.
GenGIS 2: Geospatial Analysis of Traditional and Genetic Biodiversity, with New Gradient Algorithms and an Extensible Plugin Framework
TLDR
GenGIS version 2 is introduced, which extends the linear gradient tests introduced in the first version to allow comprehensive testing of all possible linear geographic axes and implements a recently published method for biomonitoring reference condition analysis (RCA).
GenGIS: A geospatial information system for genomic data.
TLDR
The features of GenGIS are outlined and its application to georeferenced microbial metagenomic, HIV-1, and human mitochondrial DNA data sets are demonstrated.
A Phylogenomic View of Ecological Specialization in the Lachnospiraceae, a Family of Digestive Tract-Associated Bacteria
TLDR
Analysis of the genomes of 30 Lachnospiraceae isolates demonstrates that adaptation to an ecological niche and acquisition of defining functional roles within a microbiome can arise through a combination of both habitat-specific gene loss and LGT.
Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs
TLDR
The nuclear genomes of the cryptophyte Guillardia theta and the chlorarachniophyte Bigelowiella natans are sequenced and extensive genetic and biochemical mosaicism is revealed, with both host- and endosymbiont-derived genes servicing the mitochondrion, the host cell cytosol, the plastid and the remnant endosYmbionT cytOSol of both algae.
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