PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions (Q24612855)

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English	PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions	scientific article

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scholarly article

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PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions (English)

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1 reference

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inferred from title

7

object named as

Toni Gabaldón

author given names

Toni

author last names

Gabaldón

1 reference

PubMed publication ID

29 November 2023

Jaime Huerta-Cepas

1

object named as

Jaime Huerta-Cepas

author given names

Jaime

author last names

Huerta-Cepas

1 reference

PubMed publication ID

29 November 2023

object named as

Ivan Denisov

4

author given names

Ivan

author last names

Denisov

1 reference

PubMed publication ID

29 November 2023

Leszek P Pryszcz

object named as

Leszek P Pryszcz

3

author given names

Leszek P

author last names

Pryszcz

1 reference

PubMed publication ID

29 November 2023

Salvador Capella-Gutierrez

object named as

Salvador Capella-Gutierrez

2

author given names

Salvador

author last names

Capella-Gutierrez

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PubMed publication ID

29 November 2023

Marina Marcet-Houben

object named as

Marina Marcet-Houben

6

author given names

Marina

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Marcet-Houben

1 reference

PubMed publication ID

29 November 2023

author name string

Diego Kormes

5

author given names

Diego

author last names

Kormes

1 reference

PubMed publication ID

29 November 2023

language of work or name

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publication date

January 2011

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Nucleic Acids Research

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39

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Database issue

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D556-60

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copyright license

Creative Commons Attribution-NonCommercial 2.5 Generic

14 November 2016

1 reference

April 2022 Public Data File from Crossref

copyright status

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Genome sequence of the pea aphid Acyrthosiphon pisum

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3013701

7 April 2017

ETE: a python Environment for Tree Exploration

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3013701

7 April 2017

eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3013701

7 April 2017

PeroxisomeDB 2.0: an integrative view of the global peroxisomal metabolome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3013701

7 April 2017

EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3013701

7 April 2017

TreeFam: 2008 Update

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3013701

7 April 2017

PhylomeDB: a database for genome-wide collections of gene phylogenies

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3013701

7 April 2017

M-Coffee: combining multiple sequence alignment methods with T-Coffee

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3013701

7 April 2017

MUSCLE: multiple sequence alignment with high accuracy and high throughput

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3013701

7 April 2017

Fine-scale evolution: genomic, phenotypic and ecological differentiation in two coexisting Salinibacter ruber strains

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3013701

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The Jalview Java alignment editor

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3013701

7 April 2017

Identification of common molecular subsequences

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3013701

7 April 2017

Phylogenomics and the reconstruction of the tree of life

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3013701

7 April 2017

Reconstruction of the proto-mitochondrial metabolism

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3013701

7 April 2017

Phylogenomics: improving functional predictions for uncharacterized genes by evolutionary analysis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3013701

7 April 2017

The Universal Protein Resource (UniProt) in 2010

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3013701

7 April 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3013701

7 April 2017

Multiple alignment of DNA sequences with MAFFT

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3013701

7 April 2017

Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3013701

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DIALIGN-TX and multiple protein alignment using secondary structure information at GOBICS

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3013701

27 September 2017

AphidBase: a centralized bioinformatic resource for annotation of the pea aphid genome.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3013701

27 September 2017

Saccharomyces Genome Database provides mutant phenotype data.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3013701

27 September 2017

Ensembl Genomes: extending Ensembl across the taxonomic space

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3013701

27 September 2017

The tree versus the forest: the fungal tree of life and the topological diversity within the yeast phylome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3013701

27 September 2017

Large-scale assignment of orthology: back to phylogenetics?

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3013701

27 September 2017

The quest for orthologs: finding the corresponding gene across genomes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3013701

27 September 2017

The human phylome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3013701

27 September 2017

Phylogenomics: intersection of evolution and genomics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3013701

27 September 2017

A phylogenomic approach to microbial evolution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3013701

27 September 2017

MetaPhOrs: orthology and paralogy predictions from multiple phylogenetic evidence using a consistency-based confidence score.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3013701

30 May 2018

My worries are no longer behind me.

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKQ1109

21 January 2018

From phylogenetics to phylogenomics: the evolutionary relationships of insect endosymbiotic gamma-Proteobacteria as a test case.

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKQ1109

21 January 2018

The pea aphid phylome: a complete catalogue of evolutionary histories and arthropod orthology and paralogy relationships for Acyrthosiphon pisum genes.

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKQ1109

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DeathBase: a database on structure, evolution and function of proteins involved in apoptosis and other forms of cell death

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKQ1109

21 January 2018

Heads or tails: a simple reliability check for multiple sequence alignments

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https://pubmed.ncbi.nlm.nih.gov/21075798

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