A reference guide for tree analysis and visualization (Q28748327)

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scientific article (publication date: 22 February 2010)

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English	A reference guide for tree analysis and visualization	scientific article (publication date: 22 February 2010)

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instance of

scholarly article

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review article

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stated in

Europe PubMed Central

title

A reference guide for tree analysis and visualization (English)

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main subject

visualization

1 reference

based on heuristic

inferred from title

author

Adriano Barbosa-Silva

object named as

Adriano Barbosa-Silva

series ordinal

3

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Georgios A. Pavlopoulos

object named as

Georgios A Pavlopoulos

series ordinal

1

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Theodoros G Soldatos

object named as

Theodoros G Soldatos

series ordinal

2

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author name string

Reinhard Schneider

series ordinal

4

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language of work or name

English

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publication date

22 February 2010

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published in

BioData Mining

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volume

3

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issue

1

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page(s)

1

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cites work

Upcoming challenges for multiple sequence alignment methods in the high-throughput era

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PubMed Central

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2844399

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16 March 2017

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16 March 2017

Dendroscope: An interactive viewer for large phylogenetic trees

1 reference

stated in

PubMed Central

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2844399

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16 March 2017

Recent evolutions of multiple sequence alignment algorithms

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2844399

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16 March 2017

MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2844399

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16 March 2017

Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2844399

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16 March 2017

TreeDyn: towards dynamic graphics and annotations for analyses of trees

1 reference

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PubMed Central

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2844399

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16 March 2017

Toward Automatic Reconstruction of a Highly Resolved Tree of Life

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PubMed Central

reference URL

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16 March 2017

POWER: PhylOgenetic WEb Repeater--an integrated and user-optimized framework for biomolecular phylogenetic analysis

1 reference

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PubMed Central

reference URL

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16 March 2017

MUSCLE: a multiple sequence alignment method with reduced time and space complexity

1 reference

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PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2844399

retrieved

16 March 2017

MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2844399

retrieved

16 March 2017

MUSCLE: multiple sequence alignment with high accuracy and high throughput

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2844399

retrieved

16 March 2017

MrBayes 3: Bayesian phylogenetic inference under mixed models

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2844399

retrieved

16 March 2017

The Bioperl toolkit: Perl modules for the life sciences

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2844399

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16 March 2017

NEXUS: an extensible file format for systematic information

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2844399

retrieved

16 March 2017

TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2844399

retrieved

16 March 2017

MEGA2: molecular evolutionary genetics analysis software

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2844399

retrieved

16 March 2017

T-Coffee: A novel method for fast and accurate multiple sequence alignment

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2844399

retrieved

16 March 2017

Gene ontology: tool for the unification of biology

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2844399

retrieved

16 March 2017

CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2844399

retrieved

16 March 2017

Identification of common molecular subsequences

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2844399

retrieved

16 March 2017

Rapid similarity searches of nucleic acid and protein data banks

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2844399

retrieved

16 March 2017

A general method applicable to the search for similarities in the amino acid sequence of two proteins

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2844399

retrieved

16 March 2017

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

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2844399

retrieved

16 March 2017

Basic local alignment search tool

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2844399

retrieved

16 March 2017

APE: Analyses of Phylogenetics and Evolution in R language

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2844399

retrieved

7 April 2017

The Unified Medical Language System (UMLS): integrating biomedical terminology

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2844399

retrieved

7 April 2017

TM4: a free, open-source system for microarray data management and analysis

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2844399

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7 April 2017

WWW-query: an on-line retrieval system for biological sequence banks

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2844399

retrieved

7 April 2017

MEGA: Molecular Evolutionary Genetics Analysis software for microcomputers

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2844399

retrieved

7 April 2017

Arena3D: visualization of biological networks in 3D.

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2844399

retrieved

3 June 2018

PhyloWidget: web-based visualizations for the tree of life

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2844399

retrieved

3 June 2018

Approaches to comparative sequence analysis: towards a functional view of vertebrate genomes

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2844399

retrieved

3 June 2018

A general strategy to determine the congruence between a hierarchical and a non-hierarchical classification

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2844399

retrieved

3 June 2018

Three-Dimensional Phylogeny Explorer: distinguishing paralogs, lateral transfer, and violation of "molecular clock" assumption with 3D visualization

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2844399

retrieved

3 June 2018

Neighbor-joining revealed.

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2844399

retrieved

3 June 2018

Paloverde: an OpenGL 3D phylogeny browser

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2844399

retrieved

3 June 2018

An interactive power analysis tool for microarray hypothesis testing and generation

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2844399

retrieved

3 June 2018

A novel algorithm and web-based tool for comparing two alternative phylogenetic trees

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2844399

retrieved

3 June 2018

PoInTree: a polar and interactive phylogenetic tree

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2844399

retrieved

3 June 2018

Visualizations for taxonomic and phylogenetic trees

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2844399

retrieved

3 June 2018

THEA: ontology-driven analysis of microarray data

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2844399

retrieved

3 June 2018

Theoretical foundation of the balanced minimum evolution method of phylogenetic inference and its relationship to weighted least-squares tree fitting

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2844399

retrieved

3 June 2018

BAOBAB: a Java editor for large phylogenetic trees

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2844399

retrieved

3 June 2018

Optimal alignments in linear space

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2844399

retrieved

3 June 2018

Phylogenetic trees: visualizing, customizing and detecting incongruence

1 reference

stated in

Crossref

reference URL

https://api.crossref.org/works/10.1186%2F1756-0381-3-1

retrieved

21 January 2018

PAL: an object-oriented programming library for molecular evolution and phylogenetics.

1 reference

stated in

Crossref

reference URL

https://api.crossref.org/works/10.1186%2F1756-0381-3-1

retrieved

21 January 2018

TreeQ-VISTA: an interactive tree visualization tool with functional annotation query capabilities

1 reference

stated in

Crossref

reference URL

https://api.crossref.org/works/10.1186%2F1756-0381-3-1

retrieved

21 January 2018

Bootstrap Methods: Another Look at the Jackknife

1 reference

stated in

Crossref

reference URL

https://api.crossref.org/works/10.1186%2F1756-0381-3-1

retrieved

21 January 2018

PhyloGena--a user-friendly system for automated phylogenetic annotation of unknown sequences

1 reference

stated in

Crossref

reference URL

https://api.crossref.org/works/10.1186%2F1756-0381-3-1

retrieved

21 January 2018

Ordered and quantum treemaps: Making effective use of 2D space to display hierarchies

1 reference

stated in

Crossref

reference URL

https://api.crossref.org/works/10.1186%2F1756-0381-3-1

retrieved

21 January 2018

Tree visualization with tree-maps: 2-d space-filling approach

1 reference

stated in

Crossref

reference URL

https://api.crossref.org/works/10.1186%2F1756-0381-3-1

retrieved

21 January 2018

Theoretical foundation of the minimum-evolution method of phylogenetic inference.

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2844399

retrieved

27 November 2018

Hierarchical clustering schemes

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/20175922

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Modernizing the tree of life

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/20175922

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Visualizing large hierarchical clusters in hyperbolic space

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/20175922

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

CTree: comparison of clusters between phylogenetic trees made easy

1 reference

stated in

PubMed

reference URL

https://pubmed.ncbi.nlm.nih.gov/20175922

retrieved

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

DOI

10.1186/1756-0381-3-1

0 references

DBLP publication ID

journals/biodatamining/PavlopoulosSBS10

1 reference

stated in

DBLP Dataset 2021-01-02

retrieved

28 January 2021

Dimensions Publication ID

1051614296

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PMC publication ID

2844399

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PubMed publication ID

20175922

0 references

ResearchGate publication ID

41531382

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