TreeSAPP (Tree-based Sensitive and Accurate Protein Profiler) is an analysis pipeline designed to functionally and taxonomically classify protein and nucleotide sequences using marker genes and phylogenetic methods. Currently, TreeSAPP supports short read sequencing data (e.g. Illumina), but does not support long reads from newer sequencing platforms (e.g. Nanopore). Therefore, ten isolate datasets sequenced using Oxford Nanopore Technologies were aligned to reference sequences of five single-copy phylogenetic marker genes. Of the four aligners tested (minimap2, GraphMap, LAST and SNAP), minimap2 performed the best when judged by raw and weighted averages of taxonomic distance of alignments to their optimal placements, which is cruc...
Metagenomics is providing striking insights into the ecology of microbial communities. The recently ...
Abstract—The application of high performance computing methods in bioinformatics becomes increasingl...
Inferring phylogeny is a difficult computational problem. Heuristics are necessary to minimize the t...
Published onlineJournal ArticleThe phylogenetic analysis of nucleotide sequences and increasingly th...
<p>Our current understanding of the taxonomic and phylogenetic diversity of cellular organisms, espe...
MOTIVATIONMicrobial communities drive matter and energy transformations integral to global biogeoche...
Background: It has been a challenging task to build a genome-wide phylogenetic tree for a large grou...
BACKGROUND: Molecular phylogenetic methods are based on alignments of nucleic or peptidic sequences....
Summary. The problem of protein sequence classification is one of the crucial tasks in the interpret...
Abstract Background Molecular phylogenetic methods are based on alignments of nucleic or peptidic se...
Abstract.—Phylogenetic tree estimation plays a critical role in a wide variety of molecular studies,...
Microorganisms within the domains Bacteria and Archaea are the most ancient and abundant forms of li...
The phylogenetic analysis of nucleotide sequences and increasingly that of amino acid sequences is u...
Background We analyze phylogenetic tree building methods from molecular sequences (PTMS). These are...
Comparative analysis of small-subunit ribosomal RNA (ss-rRNA) gene sequences forms the basis for muc...
Metagenomics is providing striking insights into the ecology of microbial communities. The recently ...
Abstract—The application of high performance computing methods in bioinformatics becomes increasingl...
Inferring phylogeny is a difficult computational problem. Heuristics are necessary to minimize the t...
Published onlineJournal ArticleThe phylogenetic analysis of nucleotide sequences and increasingly th...
<p>Our current understanding of the taxonomic and phylogenetic diversity of cellular organisms, espe...
MOTIVATIONMicrobial communities drive matter and energy transformations integral to global biogeoche...
Background: It has been a challenging task to build a genome-wide phylogenetic tree for a large grou...
BACKGROUND: Molecular phylogenetic methods are based on alignments of nucleic or peptidic sequences....
Summary. The problem of protein sequence classification is one of the crucial tasks in the interpret...
Abstract Background Molecular phylogenetic methods are based on alignments of nucleic or peptidic se...
Abstract.—Phylogenetic tree estimation plays a critical role in a wide variety of molecular studies,...
Microorganisms within the domains Bacteria and Archaea are the most ancient and abundant forms of li...
The phylogenetic analysis of nucleotide sequences and increasingly that of amino acid sequences is u...
Background We analyze phylogenetic tree building methods from molecular sequences (PTMS). These are...
Comparative analysis of small-subunit ribosomal RNA (ss-rRNA) gene sequences forms the basis for muc...
Metagenomics is providing striking insights into the ecology of microbial communities. The recently ...
Abstract—The application of high performance computing methods in bioinformatics becomes increasingl...
Inferring phylogeny is a difficult computational problem. Heuristics are necessary to minimize the t...