(Q34607738)

25525323

3 August 2017

title

SWAMP: Sliding Window Alignment Masker for PAML. (English)

1 reference

3 August 2017

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25525323%20AND%20SRC:MED&resulttype=core&format=json

12 June 2020

Stephen H Montgomery

series ordinal

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25525323%20AND%20SRC:MED&resulttype=core&format=json

12 June 2020

author name string

Gregory E Jordan

series ordinal

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25525323%20AND%20SRC:MED&resulttype=core&format=json

12 June 2020

publication date

1 December 2014

1 reference

25525323

Evolutionary Bioinformatics

3 August 2017

published in

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25525323%20AND%20SRC:MED&resulttype=core&format=json

12 June 2020

volume

10

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25525323%20AND%20SRC:MED&resulttype=core&format=json

12 June 2020

page(s)

197-204

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25525323%20AND%20SRC:MED&resulttype=core&format=json

12 June 2020

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4251194

Masculinization of gene expression is associated with exaggeration of male sexual dimorphism

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4251194

Dolphin genome provides evidence for adaptive evolution of nervous system genes and a molecular rate slowdown

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4251194

Insights into hominid evolution from the gorilla genome sequence

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4251194

Trans genomic capture and sequencing of primate exomes reveals new targets of positive selection

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4251194

Biases in Illumina transcriptome sequencing caused by random hexamer priming

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4251194

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4251194

Estimates of positive Darwinian selection are inflated by errors in sequencing, annotation, and alignment.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4251194

An alignment confidence score capturing robustness to guide tree uncertainty

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4251194

Next-generation DNA sequencing

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4251194

Patterns of positive selection in six Mammalian genomes

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4251194

Substantial biases in ultra-short read data sets from high-throughput DNA sequencing

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4251194

Noisy: identification of problematic columns in multiple sequence alignments

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4251194

Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4251194

Alignment uncertainty and genomic analysis

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4251194

Accuracy and quality of massively parallel DNA pyrosequencing

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4251194

PAML 4: phylogenetic analysis by maximum likelihood

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4251194

Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4251194

A scan for positively selected genes in the genomes of humans and chimpanzees

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4251194

ProbCons: Probabilistic consistency-based multiple sequence alignment

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4251194

MAFFT version 5: improvement in accuracy of multiple sequence alignment

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4251194

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4251194

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4251194

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4251194

SINEs and LINEs: Highly repeated short and long interspersed sequences in mammalian genomes

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4251194

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4251194

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

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4251194

The difficulty of avoiding false positives in genome scans for natural selection

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4251194

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

26 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25525323

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.4137/EBO.S18193

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25525323%20AND%20SRC:MED&resulttype=core&format=json

12 June 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25525323%20AND%20SRC:MED&resulttype=core&format=json

12 June 2020

25525323

1 reference