(Q28654410)

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Orthology inference in nonmodel organisms using transcriptomes and low-coverage genomes: improving accuracy and matrix occupancy for phylogenomics

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scholarly article

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Europe PubMed Central

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25158799%20AND%20SRC:MED&resulttype=core&format=json

13 March 2020

Orthology inference in nonmodel organisms using transcriptomes and low-coverage genomes: improving accuracy and matrix occupancy for phylogenomics (English)

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Europe PubMed Central

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25158799%20AND%20SRC:MED&resulttype=core&format=json

13 March 2020

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Stephen A. Smith

2

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Europe PubMed Central

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25158799%20AND%20SRC:MED&resulttype=core&format=json

13 March 2020

author name string

Ya Yang

1

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Europe PubMed Central

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25158799%20AND%20SRC:MED&resulttype=core&format=json

13 March 2020

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25 August 2014

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13 March 2020

Molecular Biology and Evolution

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13 March 2020

31

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13 March 2020

11

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25158799%20AND%20SRC:MED&resulttype=core&format=json

13 March 2020

3081-3092

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Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25158799%20AND%20SRC:MED&resulttype=core&format=json

13 March 2020

Ordinal-level phylogenomics of the arthropod class Diplopoda (millipedes) based on an analysis of 221 nuclear protein-coding loci generated using next-generation sequence analyses

1 reference

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Phylogenomics resolves evolutionary relationships among ants, bees, and wasps

1 reference

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17 March 2017

Transcriptome sequences resolve deep relationships of the grape family

1 reference

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

1 reference

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MACSE: Multiple Alignment of Coding SEquences accounting for frameshifts and stop codons

1 reference

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1 reference

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1 reference

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1 reference

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1 reference

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OMA 2011: orthology inference among 1000 complete genomes

1 reference

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17 March 2017

Genomic comparison of the ants Camponotus floridanus and Harpegnathos saltator

1 reference

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FastTree 2--approximately maximum-likelihood trees for large alignments

1 reference

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Functional and evolutionary insights from the genomes of three parasitoid Nasonia species

1 reference

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17 March 2017

Broad phylogenomic sampling improves resolution of the animal tree of life

1 reference

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17 March 2017

The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla

1 reference

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17 March 2017

Insights into social insects from the genome of the honeybee Apis mellifera

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4209138

17 March 2017

RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4209138

17 March 2017

TreeFam: a curated database of phylogenetic trees of animal gene families

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4209138

17 March 2017

OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4209138

17 March 2017

An efficient algorithm for large-scale detection of protein families

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4209138

17 March 2017

Basic local alignment search tool

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4209138

17 March 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4209138

7 April 2017

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4209138

7 April 2017

CD-HIT: accelerated for clustering the next-generation sequencing data

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4209138

7 April 2017

Phytozome: a comparative platform for green plant genomics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4209138

7 April 2017

Distinguishing Homologous from Analogous Proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4209138

7 April 2017

Homology a personal view on some of the problems

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4209138

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The draft genome of a socially polymorphic halictid bee, Lasioglossum albipes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4209138

20 June 2018

Agalma: an automated phylogenomics workflow

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4209138

20 June 2018

Optimizing de novo assembly of short-read RNA-seq data for phylogenomics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4209138

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Convergent gene loss following gene and genome duplications creates single-copy families in flowering plants

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4209138

20 June 2018

Inferring hierarchical orthologous groups from orthologous gene pairs

1 reference

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20 June 2018

Genome-scale coestimation of species and gene trees.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4209138

20 June 2018

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1 reference

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20 June 2018

VectorBase: improvements to a bioinformatics resource for invertebrate vector genomics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4209138

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1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4209138

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1 reference

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1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4209138

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1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4209138

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1 reference

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1 reference

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1 reference

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1 reference

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1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU245

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1 reference

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1 reference

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1 reference

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1 reference

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1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU245

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1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU245

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1 reference

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27 November 2018

Identifiers

10.1093/MOLBEV/MSU245

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Consolidated OpenCitations Corpus – April 2017

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Europe PubMed Central

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25158799%20AND%20SRC:MED&resulttype=core&format=json

13 March 2020

OpenCitations bibliographic resource ID

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Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

PMC publication ID

2 references

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25158799%20AND%20SRC:MED&resulttype=core&format=json

13 March 2020

PubMed publication ID

2 references

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25158799%20AND%20SRC:MED&resulttype=core&format=json

13 March 2020

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