Metagenomic analysis using phylogenetic placement—a review of the first decade
Phylogenetic placement refers to a family of tools and methods to analyze, visualize, and
interpret the tsunami of metagenomic sequencing data generated by high-throughput …
interpret the tsunami of metagenomic sequencing data generated by high-throughput …
Fast and accurate distance‐based phylogenetic placement using divide and conquer
Phylogenetic placement of query samples on an existing phylogeny is increasingly used in
molecular ecology, including sample identification and microbiome environmental sampling …
molecular ecology, including sample identification and microbiome environmental sampling …
Quantifying the uncertainty of assembly-free genome-wide distance estimates and phylogenetic relationships using subsampling
Computing distance between two genomes without alignments or even access to
assemblies has many downstream analyses. However, alignment-free methods, including in …
assemblies has many downstream analyses. However, alignment-free methods, including in …
CONSULT: accurate contamination removal using locality-sensitive hashing
A fundamental question appears in many bioinformatics applications: Does a sequencing
read belong to a large dataset of genomes from some broad taxonomic group, even when …
read belong to a large dataset of genomes from some broad taxonomic group, even when …
De novo genome assembly and annotation of the medicinal plant Tinospora cordifolia (Willd.) Miers ex Hook. f. & Thom's
M KH, SN Hegde, N Begum, SK Kukkupuni… - Functional & Integrative …, 2023 - Springer
Indian natural climbing shrub Tinospora cordifolia, often known as “Guduchi” and “Amrita,” is
a highly esteemed medicinal plant in the Indian system of medicine (ISM). It is a member of …
a highly esteemed medicinal plant in the Indian system of medicine (ISM). It is a member of …
Genome-wide alignment-free phylogenetic distance estimation under a no strand-bias model
While alignment has been the dominant approach for determining homology prior to
phylogenetic inference, alignment-free methods can simplify the analysis, especially when …
phylogenetic inference, alignment-free methods can simplify the analysis, especially when …
Analyses of Nuclear Reads Obtained Using Genome Skimming
In this protocol paper, we review a set of methods developed in recent years for analyzing
nuclear reads obtained from genome skimming. As the cost of sequencing drops, genome …
nuclear reads obtained from genome skimming. As the cost of sequencing drops, genome …
Distance-based phylogenetic placement with statistical support
Simple Summary Phylogenetic placement seeks to find the optimal position for a new query
species on an existing backbone tree. Fast and accurate distance-based phylogenetic …
species on an existing backbone tree. Fast and accurate distance-based phylogenetic …
Fast and accurate branch support calculation for distance-based phylogenetic placements
Placing a new sequence onto an existing phylogenetic tree is increasingly used in
downstream applications ranging from microbiome analyses to epidemic tracking. Most such …
downstream applications ranging from microbiome analyses to epidemic tracking. Most such …
[LIBRO][B] Alignment-free genomic distance estimation: from conventional methods to machine learning
E Rachtman - 2023 - search.proquest.com
Inferring evolutionary relationships based on comparative analysis of genomic data remains
a fundamental question in biology. Conventionally, these analyses involve cumbersome and …
a fundamental question in biology. Conventionally, these analyses involve cumbersome and …