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Các bài báo tiêu biểu
VSEARCH: a versatile open source tool for metagenomics
Tập 4 - Trang e2584
BackgroundVSEARCH is an open source and free of charge multithreaded 64-bit tool
for processing and preparing metagenomics, genomics and population genomics
nucleotide sequence data. It is designed as an alternative to the widely used
USEARCH tool (Edgar, 2010) for which the source code is not publicly available,
algorithm details are only rudimentarily described, and only a memory-confined
32-bit...
MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities
Tập 3 - Trang e1165
A brief introduction to mixed effects modelling and multi-model inference in ecology
Tập 6 - Trang e4794
The use of linear mixed effects models (LMMs) is increasingly common in the
analysis of biological data. Whilst LMMs offer a flexible approach to modelling
a broad range of data types, ecological data are often complex and require
complex model structures, and the fitting and interpretation of such models is
not always straightforward. The ability to achieve robust biological inference
requires th...
SDMtoolbox 2.0: the next generation Python-based GIS toolkit for landscape genetic, biogeographic and species distribution model analyses
Tập 5 - Trang e4095
SDMtoolbox 2.0 is a software package for spatial studies of ecology, evolution,
and genetics. The release of SDMtoolbox 2.0 allows researchers to use the most
current ArcGIS software and MaxEnt software, and reduces the amount of time that
would be spent developing common solutions. The central aim of this software is
to automate complicated and repetitive spatial analyses in an intuitive
graphica...
MaxEnt’s parameter configuration and small samples: are we paying attention to recommendations? A systematic review
Tập 5 - Trang e3093
Environmental niche modeling (ENM) is commonly used to develop probabilistic
maps of species distribution. Among available ENM techniques, MaxEnt has become
one of the most popular tools for modeling species distribution, with hundreds
of peer-reviewed articles published each year. MaxEnt’s popularity is mainly due
to the use of a graphical interface and automatic parameter configuration
capabilit...
Rhea: a transparent and modular R pipeline for microbial profiling based on 16S rRNA gene amplicons
Tập 5 - Trang e2836
The importance of 16S rRNA gene amplicon profiles for understanding the
influence of microbes in a variety of environments coupled with the steep
reduction in sequencing costs led to a surge of microbial sequencing projects.
The expanding crowd of scientists and clinicians wanting to make use of
sequencing datasets can choose among a range of multipurpose software platforms,
the use of which can b...
Leopard (Panthera pardus) status, distribution, and the research efforts across its range
Tập 4 - Trang e1974
The leopard’s (Panthera pardus) broad geographic range, remarkable adaptability,
and secretive nature have contributed to a misconception that this species might
not be severely threatened across its range. We find that not only are several
subspecies and regional populations critically endangered but also the overall
range loss is greater than the average for terrestrial large carnivores. To
asse...
De novo clustering methods outperform reference-based methods for assigning 16S rRNA gene sequences to operational taxonomic units
Tập 3 - Trang e1487
Background.16S rRNA gene sequences are routinely assigned to operational
taxonomic units (OTUs) that are then used to analyze complex microbial
communities. A number of methods have been employed to carry out the assignment
of 16S rRNA gene sequences to OTUs leading to confusion over which method is
optimal. A recent study suggested that a clustering method should be selected
based on its ability ...