(Q38695928)

PubMed publication ID

5 September 2017

2 references

30 October 2020

Alignment-free inference of hierarchical and reticulate phylogenomic relationships (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=PMCID:PMC6433738&resulttype=core&format=json

13 May 2020

1 reference

1 reference

30 October 2020

7

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=PMCID:PMC6433738&resulttype=core&format=json

13 May 2020

author name string

Guillaume Bernard

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=PMCID:PMC6433738&resulttype=core&format=json

13 May 2020

Cheong Xin Chan

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=PMCID:PMC6433738&resulttype=core&format=json

13 May 2020

Yao-Ban Chan

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=PMCID:PMC6433738&resulttype=core&format=json

13 May 2020

Xin-Yi Chua

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=PMCID:PMC6433738&resulttype=core&format=json

13 May 2020

Yingnan Cong

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=PMCID:PMC6433738&resulttype=core&format=json

13 May 2020

James M Hogan

6

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=PMCID:PMC6433738&resulttype=core&format=json

13 May 2020

Mark A Ragan

8

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=PMCID:PMC6433738&resulttype=core&format=json

13 May 2020

publication date

30 June 2017

1 reference

PubMed publication ID

28673025

Briefings in Bioinformatics

5 September 2017

22 March 2019

1 reference

30 October 2020

2 references

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=PMCID:PMC6433738&resulttype=core&format=json

13 May 2020

30 October 2020

20

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=PMCID:PMC6433738&resulttype=core&format=json

13 May 2020

issue

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=PMCID:PMC6433738&resulttype=core&format=json

13 May 2020

page(s)

426-435

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=PMCID:PMC6433738&resulttype=core&format=json

Creative Commons Attribution 4.0 International

13 May 2020

copyright license

1 reference

describes a project that uses

30 October 2020

copyright status

copyrighted

0 references

MUMmer

object named as

MUMmer

1 reference

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

cites work

Phylogenomics and the reconstruction of the tree of life

1 reference

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Phylogenomics: intersection of evolution and genomics

21 January 2018

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A case for evolutionary genomics and the comprehensive examination of sequence biodiversity.

21 January 2018

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A phylogenomic approach to microbial evolution

21 January 2018

1 reference

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Molecular phylogenetics before sequences: oligonucleotide catalogs as k-mer spectra

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX067

Progressive sequence alignment as a prerequisite to correct phylogenetic trees

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX067

Next-generation phylogenomics

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX067

An assembly and alignment-free method of phylogeny reconstruction from next-generation sequencing data

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX067

progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX067

Alignathon: a competitive assessment of whole-genome alignment methods

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX067

Highways of gene sharing in prokaryotes

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX067

Horizontal gene transfer, genome innovation and evolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX067

Are protein domains modules of lateral genetic transfer?

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX067

Amelioration of bacterial genomes: rates of change and exchange

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX067

Prokaryotic evolution in light of gene transfer

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX067

Within-species lateral genetic transfer and the evolution of transcriptional regulation in Escherichia coli and Shigella.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX067

Biological evaluation of d2, an algorithm for high-performance sequence comparison.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX067

A comprehensive approach to clustering of expressed human gene sequence: the sequence tag alignment and consensus knowledge base.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX067

Iterative error correction of long sequencing reads maximizes accuracy and improves contig assembly

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX067

How to apply de Bruijn graphs to genome assembly

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX067

A method to predict the impact of regulatory variants from DNA sequence

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX067

Discriminative prediction of mammalian enhancers from DNA sequence.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX067

An alignment-free test for recombination

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX067

Alignment-free phylogenetics and population genetics

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX067

Alignment-free sequence comparison-a review

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX067

A novel alignment-free method for detection of lateral genetic transfer based on TF-IDF.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX067

Exploring lateral genetic transfer among microbial genomes using TF-IDF.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX067

Dictionary-driven protein annotation

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX067

A visual framework for sequence analysis using n-grams and spectral rearrangement

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX067

From Ukkonen to McCreight and Weiner: A Unifying View of Linear-Time Suffix Tree Construction

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX067

Suffix Arrays: A New Method for On-Line String Searches

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX067

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX067

Blue: correcting sequencing errors using consensus and context.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX067

Efficient counting of k-mers in DNA sequences using a bloom filter

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX067

Space/time trade-offs in hash coding with allowable errors

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX067

Bloom Filter Trie: an alignment-free and reference-free data structure for pan-genome storage

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX067

Alignment of whole genomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX067

Aggressive assembly of pyrosequencing reads with mates

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX067

A new method to compute K-mer frequencies and its application to annotate large repetitive plant genomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX067

Whole-proteome phylogeny of prokaryotes by feature frequency profiles: An alignment-free method with optimal feature resolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX067

Alignment-free sequence comparison (I): statistics and power

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX067

A grammar-based distance metric enables fast and accurate clustering of large sets of 16S sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX067

A fungal phylogeny based on 82 complete genomes using the composition vector method

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX067

Phylogeny Reconstruction with Alignment-Free Method That Corrects for Horizontal Gene Transfer

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX067

Estimation of pairwise sequence similarity of mammalian enhancers with word neighbourhood counts

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX067

Co-phylog: an assembly-free phylogenomic approach for closely related organisms

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX067

The average common substring approach to phylogenomic reconstruction

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX067

Estimating mutation distances from unaligned genomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX067

Distributional regimes for the number of k-word matches between two random sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX067

New developments of alignment-free sequence comparison: measures, statistics and next-generation sequencing

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX067

A measure of the similarity of sets of sequences not requiring sequence alignment

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX067

Alignment-free sequence comparison (II): theoretical power of comparison statistics

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX067

The distribution of word matches between Markovian sequences with periodic boundary conditions.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX067

Genomic DNA k-mer spectra: models and modalities

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX067

Is multiple-sequence alignment required for accurate inference of phylogeny?

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX067

PAML 4: phylogenetic analysis by maximum likelihood

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX067

Alignment-free microbial phylogenomics under scenarios of sequence divergence, genome rearrangement and lateral genetic transfer

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX067

Spaced words and kmacs: fast alignment-free sequence comparison based on inexact word matches

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX067

Whole-genome phylogeny of Escherichia coli/Shigella group by feature frequency profiles (FFPs)

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX067

Recapitulating phylogenies using k-mers: from trees to networks

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX067

Detecting lateral genetic transfer : a phylogenetic approach.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX067

Scaling Up the Phylogenetic Detection of Lateral Gene Transfer Events.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX067

Detecting recombination in evolving nucleotide sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX067

Inferring genome trees by using a filter to eliminate phylogenetically discordant sequences and a distance matrix based on mean normalized BLASTP scores

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX067

Detection of lateral gene transfer among microbial genomes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX067

On surrogate methods for detecting lateral gene transfer

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX067

ALF--a simulation framework for genome evolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX067

A benchmark of parametric methods for horizontal transfers detection

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX067

Detection and characterization of horizontal transfers in prokaryotes using genomic signature

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX067

Horizontal gene transfer in bacterial and archaeal complete genomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX067

Molecular archaeology of the Escherichia coli genome

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX067

Evidence for horizontal gene transfer in Escherichia coli speciation

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX067

Do different surrogate methods detect lateral genetic transfer events of different relative ages?

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX067

Detection of horizontal transfer of individual genes by anomalous oligomer frequencies

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX067

21 January 2018

Manuscript evolution.

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX067

On the Reconstruction of Text Phylogeny Trees: Evaluation and Analysis of Textual Relationships

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX067

Alignment-free genome comparison with feature frequency profiles (FFP) and optimal resolutions

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX067

Lateral genetic transfer and the construction of genetic exchange communities

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX067

Network analyses structure genetic diversity in independent genetic worlds

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX067

Getting a better picture of microbial evolution en route to a network of genomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX067

The horizontal flow of the plasmid resistome: clues from inter-generic similarity networks

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX067

The Turbulent Network Dynamics of Microbial Evolution and the Statistical Tree of Life

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX067

The tree and net components of prokaryote evolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX067

MACHOS: Markov clusters of homologous subsequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX067

An efficient algorithm for large-scale detection of protein families

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX067

Towards the mammalian interactome: Inference of a core mammalian interaction set in mouse

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX067

The practice of classification and the theory of evolution, and what the demise of Charles Darwin's tree of life hypothesis means for both of them

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX067

Pattern pluralism and the Tree of Life hypothesis

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX067

A note on the neighbor-joining algorithm of Saitou and Nei.

21 January 2018

1 reference

12 December 2020

Detecting communities based on network topology

1 reference

12 December 2020

Characterizing the D2 statistic: word matches in biological sequences

1 reference

12 December 2020

Fast and accurate phylogeny reconstruction using filtered spaced-word matches.

1 reference

12 December 2020

Homology: A Definition

1 reference

12 December 2020

The neighbor-joining method: a new method for reconstructing phylogenetic trees

1 reference

12 December 2020

Inferring phylogenies of evolving sequences without multiple sequence alignment.

1 reference

12 December 2020

Pattern-based phylogenetic distance estimation and tree reconstruction.

1 reference

12 December 2020

Robust Inference of Genetic Exchange Communities from Microbial Genomes Using TF-IDF.

1 reference

12 December 2020

A simulation test bed for hypotheses of genome evolution

1 reference

12 December 2020

Alignment-free sequence comparison for biologically realistic sequences of moderate length

1 reference

12 December 2020

Lateral transfer of genes and gene fragments in prokaryotes

1 reference

12 December 2020

Identifiers

DOI

10.1093/BIB/BBX067

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=PMCID:PMC6433738&resulttype=core&format=json

journals/bib/BernardCCCCHMR19

13 May 2020

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=PMCID:PMC6433738&resulttype=core&format=json

13 May 2020

PubMed publication ID

28673025

1 reference