ReproPhylo: An Environment for Reproducible Phylogenomics (Q35763503)

10 August 2017

title

ReproPhylo: An Environment for Reproducible Phylogenomics. (English)

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10 August 2017

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4

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Mark Blaxter

object named as

Mark L Blaxter

series ordinal

3

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author name string

Amir Szitenberg

series ordinal

1

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10 August 2017

Max John

series ordinal

2

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10 August 2017

publication date

3 September 2015

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PLOS Computational Biology

10 August 2017

published in

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10 August 2017

volume

11

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10 August 2017

issue

9

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10 August 2017

page(s)

e1004447

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Creative Commons Attribution 4.0 International

10 August 2017

copyright license

start time

3 September 2015

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April 2022 Public Data File from Crossref

copyright status

copyrighted

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describes a project that uses

Jupyter notebook file

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Reproducibility in science: improving the standard for basic and preclinical research

cites work

1 reference

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2 October 2017

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Mating system shifts and transposable element evolution in the plant genus Capsella

2 October 2017

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2 October 2017

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Best practices for data sharing in phylogenetic research

2 October 2017

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Phylogenomics provides strong evidence for relationships of butterflies and moths

2 October 2017

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Building a phylogenomic pipeline for the eukaryotic tree of life - addressing deep phylogenies with genome-scale data

2 October 2017

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2 October 2017

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2 October 2017

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The Availability of Research Data Declines Rapidly with Article Age

2 October 2017

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Agalma: an automated phylogenomics workflow

2 October 2017

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MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

2 October 2017

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Anchored hybrid enrichment for massively high-throughput phylogenomics

2 October 2017

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4559436

Phylemon 2.0: a suite of web-tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing

2 October 2017

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CDAO-store: ontology-driven data integration for phylogenetic analysis

2 October 2017

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Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

2 October 2017

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DendroPy: a Python library for phylogenetic computing

2 October 2017

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ETE: a python Environment for Tree Exploration

2 October 2017

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Galaxy: a web-based genome analysis tool for experimentalists

2 October 2017

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phyloXML: XML for evolutionary biology and comparative genomics

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4559436

PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating

2 October 2017

1 reference

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trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

2 October 2017

1 reference

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Biopython: freely available Python tools for computational molecular biology and bioinformatics

2 October 2017

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Methodology capture: discriminating between the "best" and the rest of community practice

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4559436

Phylogeny.fr: robust phylogenetic analysis for the non-specialist

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4559436

Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4559436

Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA)

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4559436

PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4559436

Galaxy: a platform for interactive large-scale genome analysis

2 October 2017

1 reference

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Automated generation of heuristics for biological sequence comparison

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4559436

Bayesian estimation of ancestral character states on phylogenies

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4559436

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

2 October 2017

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MUSCLE: multiple sequence alignment with high accuracy and high throughput

2 October 2017

1 reference

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Ontologies for molecular biology and bioinformatics

2 October 2017

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Scoring residue conservation

2 October 2017

1 reference

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RNA secondary structure: physical and computational aspects

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4559436

A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4559436

A role for nonadaptive processes in plant genome size evolution?

2 October 2017

1 reference

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IPython: A System for Interactive Scientific Computing

25 September 2018

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21 January 2018

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https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1004447

Matplotlib: A 2D Graphics Environment

21 January 2018

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https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1004447

A mathematical theory of communication

21 January 2018

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https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1004447

phyloGenerator: an automated phylogeny generation tool for ecologists

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1004447

Journals unite for reproducibility

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26335558

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PCBI.1004447

1 reference

journals/ploscb/SzitenbergJBL15

10 August 2017

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

10 August 2017

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