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Data from: Phylogenetic tree estimation with and without alignment: new distance methods and benchmarking
负责人:
关键词:
Pair hidden Markov models;phylogenetic inference;Alignment free;Distance-based phylogenetics;statistical alignment
DOI:
doi:10.5061/dryad.n5r49
摘要:
d on the two-step process of multiple sequence alignment followed by tree inference, despite persistent evidence that the alignment step can lead to biased results. Her
Data from: Not all sequence tags are created equal: designing and validating sequence identification tags robust to indels
负责人:
关键词:
Hamming distance;edit metric;sequence tags;Levenshtein distance;massively parallel sequencing
DOI:
doi:10.5061/dryad.4m0v8474
摘要:
Ligating adapters with unique synthetic oligonucleotide sequences (sequence tags) onto individual DNA samples before massively parallel sequencing
Data from: Simple chained guide trees give poorer multiple sequence alignments than inferred trees in simulation and phylogenetic benchmarks
负责人:
关键词:
guide tree;sequence alignment;phylogeny;MSA;benchmark
DOI:
doi:10.5061/dryad.4r5b8
摘要:
Multiple sequence aligners typically work by progressively aligning the most closely related sequences or group of sequences according to guide trees
Data from: SNPdryad: predicting deleterious non-synonymous human SNPs using only orthologous protein sequences
负责人:
关键词:
DOI:
doi:10.5061/dryad.n7m28
摘要:
h prediction algorithms depends on the quality of the multiple-sequence alignment, which is used to infer how an amino acid substitution is tolerated at a given position
Data from: Current methods for automated filtering of multiple sequence alignments frequently worsen single-gene phylogenetic inference
负责人:
关键词:
phylogenetic inference;alignment trimming;multiple sequence alignment;alignment filtering;molecular phylogeny;phylogenetics;phylogeny
DOI:
doi:10.5061/dryad.pc5j0
摘要:
Phylogenetic inference is generally performed on the basis of multiple sequence alignments (MSA). Because errors in an alignment can lead to errors
Data from: A simulation-based approach to statistical alignment
负责人:
关键词:
statistical alignment;pairwise alignment;long-indel model;SimBa-SAl;sequence simulations
DOI:
doi:10.5061/dryad.p069231
摘要:
. Finally, it allows computing the maximum-likelihood alignment, the probability of a given pair of sequences integrated over all possible alignment
Data from: Multiple sequence alignment averaging improves phylogeny reconstruction
负责人:
关键词:
Alignment reliability;multiple sequence alignment;phylogeny;Tree reconstruction
DOI:
doi:10.5061/dryad.4j1qt
摘要:
The classic methodology of inferring a phylogenetic tree from sequence data is composed of two steps. First, a multiple sequence alignment (MSA
Data from: Construction of a virtual Mycobacterium tuberculosis consensus genome and its application to data from a next generation sequencer
负责人:
关键词:
phylogenetic analysis;Mycobacterium tuberculosis;consensus sequence;virtual typing;SNP concatemer
DOI:
doi:10.5061/dryad.nq070
摘要:
of the M. tuberculosis complexes (MTBCs) strains available on databases were aligned to construct virtual reference genome sequences called the consensus sequence (CS
Data from: Aligner optimization increases accuracy and decreases compute times in multi-species sequence data
负责人:
关键词:
Plasmodium falciparum;alignments;Brugia malayi;Wolbachia;metagenomics;bioinformatics;genomics;Homo Sapiens;parasite genomics;dual species RNASeq;microbial genomics
DOI:
doi:10.5061/dryad.m1m0p
摘要:
, we observed important and adverse differences in alignment specificity and computation time for bwa- mem (Burrows–Wheeler aligner-maximum exact matches

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