(Q30661502)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26031838%20AND%20SRC:MED&resulttype=core&format=json

16 February 2020

title

Current Methods for Automated Filtering of Multiple Sequence Alignments Frequently Worsen Single-Gene Phylogenetic Inference (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26031838%20AND%20SRC:MED&resulttype=core&format=json

16 February 2020

1 reference

1 reference

1 reference

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26031838%20AND%20SRC:MED&resulttype=core&format=json

16 February 2020

Javier Herrero

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26031838%20AND%20SRC:MED&resulttype=core&format=json

16 February 2020

Nick Goldman

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26031838%20AND%20SRC:MED&resulttype=core&format=json

16 February 2020

Christophe Dessimoz

7

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26031838%20AND%20SRC:MED&resulttype=core&format=json

16 February 2020

Ge Tan

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26031838%20AND%20SRC:MED&resulttype=core&format=json

16 February 2020

author name string

Christian Ledergerber

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26031838%20AND%20SRC:MED&resulttype=core&format=json

16 February 2020

Manuel Gil

6

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26031838%20AND%20SRC:MED&resulttype=core&format=json

16 February 2020

publication date

1 June 2015

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26031838%20AND%20SRC:MED&resulttype=core&format=json

16 February 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26031838%20AND%20SRC:MED&resulttype=core&format=json

16 February 2020

volume

64

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26031838%20AND%20SRC:MED&resulttype=core&format=json

16 February 2020

issue

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26031838%20AND%20SRC:MED&resulttype=core&format=json

16 February 2020

page(s)

778-791

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26031838%20AND%20SRC:MED&resulttype=core&format=json

Who watches the watchmen? An appraisal of benchmarks for multiple sequence alignment.

16 February 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4538881

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4538881

Impact of missing data on phylogenies inferred from empirical phylogenomic data sets

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4538881

Accounting for alignment uncertainty in phylogenomics

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4538881

ALF--a simulation framework for genome evolution

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4538881

Survey of branch support methods demonstrates accuracy, power, and robustness of fast likelihood-based approximation schemes

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4538881

OMA 2011: orthology inference among 1000 complete genomes

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4538881

Quantifying the impact of dependent evolution among sites in phylogenetic inference

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4538881

BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4538881

New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4538881

Sparse supermatrices for phylogenetic inference: taxonomy, alignment, rogue taxa, and the phylogeny of living turtles

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4538881

GUIDANCE: a web server for assessing alignment confidence scores.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4538881

Phylogenetic assessment of alignments reveals neglected tree signal in gaps

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4538881

Parametric and non-parametric masking of randomness in sequence alignments can be improved and leads to better resolved trees

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4538881

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4538881

Database resources of the National Center for Biotechnology Information

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4538881

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4538881

Fast statistical alignment

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4538881

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4538881

StatAlign: an extendable software package for joint Bayesian estimation of alignments and evolutionary trees

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4538881

Noisy: identification of problematic columns in multiple sequence alignments

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4538881

DIALIGN-TX: greedy and progressive approaches for segment-based multiple sequence alignment

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4538881

Alignment uncertainty and genomic analysis

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4538881

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4538881

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4538881

BAli-Phy: simultaneous Bayesian inference of alignment and phylogeny

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4538881

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4538881

Kalign--an accurate and fast multiple sequence alignment algorithm

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4538881

An algorithm for progressive multiple alignment of sequences with insertions

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4538881

MAFFT version 5: improvement in accuracy of multiple sequence alignment

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4538881

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4538881

MrBayes 3: Bayesian phylogenetic inference under mixed models

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4538881

A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4538881

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4538881

Darwin v. 2.0: an interpreted computer language for the biosciences

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4538881

Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4538881

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4538881

Distinguishing Homologous from Analogous Proteins

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4538881

Dating of the human-ape splitting by a molecular clock of mitochondrial DNA

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4538881

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4538881

The effects of alignment error and alignment filtering on the sitewise detection of positive selection.

20 June 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV033

Uncertainty in homology inferences: assessing and improving genomic sequence alignment

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV033

Improving the performance of positive selection inference by filtering unreliable alignment regions.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV033

Large-scale comparison of protein sequence alignment algorithms with structure alignments

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV033

A simple algorithm to infer gene duplication and speciation events on a gene tree.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV033

Why would phylogeneticists ignore computerized sequence alignment?

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26031838

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

The effect of insertions, deletions, and alignment errors on the branch-site test of positive selection

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26031838

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

BAliBASE 3.0: latest developments of the multiple sequence alignment benchmark

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26031838

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/SYSBIO/SYV033

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26031838%20AND%20SRC:MED&resulttype=core&format=json

16 February 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26031838%20AND%20SRC:MED&resulttype=core&format=json

16 February 2020

PubMed publication ID

26031838

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26031838%20AND%20SRC:MED&resulttype=core&format=json