MBEToolbox: a MATLAB toolbox for sequence data analysis in molecular biology and evolution (Q24811533)

Europe PubMed Central

title

MBEToolbox: a MATLAB toolbox for sequence data analysis in molecular biology and evolution (English)

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4

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ORCID Public Data File 2021

James J. Cai

object named as

James J Cai

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1

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Xuhua Xia

object named as

Xuhua Xia

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3

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author name string

David K Smith

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2

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language of work or name

English

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publication date

2005

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published in

BMC Bioinformatics

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volume

6

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issue

1

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page(s)

64

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exact match

https://scigraph.springernature.com/pub.10.1186/1471-2105-6-64

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cites work

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1274259

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

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1274259

Improved tools for biological sequence comparison

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1274259

A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1274259

Evolutionary trees from DNA sequences: A maximum likelihood approach

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1274259

Identification of common molecular subsequences

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1274259

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

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1274259

Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1274259

Evolution of the Zfx and Zfy genes: rates and interdependence between the genes

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1274259

Unbiased estimation of the rates of synonymous and nonsynonymous substitution

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1274259

Z curves, an intutive tool for visualizing and analyzing the DNA sequences

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1274259

A new method for estimating synonymous and nonsynonymous rates of nucleotide substitution considering the relative likelihood of nucleotide and codon changes

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1274259

A new method for calculating evolutionary substitution rates

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1274259

The general stochastic model of nucleotide substitution

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1274259

Adaptive Evolution of MRG, a Neuron-Specific Gene Family Implicated in Nociception

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1274259

MatArray: a Matlab toolbox for microarray data

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1274259

Within- and between-species DNA sequence variation and the 'footprint' of natural selection

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1274259

Parallel evolution of drug resistance in HIV: failure of nonsynonymous/synonymous substitution rate ratio to detect selection

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1274259

Reconstructing evolutionary trees from DNA and protein sequences: paralinear distances

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1274259

Excess nonsynonymous substitution of shared polymorphic sites among self-incompatibility alleles of Solanaceae

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1274259

Detecting selection using a single genome sequence of M. tuberculosis and P. falciparum

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1274259

Markov chain Monte Carlo computation of confidence intervals for substitution-rate variation in proteins.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1274259

Large-scale search for genes on which positive selection may operate.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1274259

ODEN: a program package for molecular evolutionary analysis and database search of DNA and amino acid sequences

28 November 2018

1 reference

12 December 2020

Estimating the pattern of nucleotide substitution

1 reference

12 December 2020

In search of molecular darwinism

1 reference

12 December 2020

A novel method to calculate the G+C content of genomic DNA sequences

1 reference

12 December 2020

Identifiers

DOI

10.1186/1471-2105-6-64

1 reference

5036450

DBLP publication ID

journals/bmcbi/CaiSXY05

1 reference

DBLP Dataset 2021-01-02

Dimensions Publication ID

28 January 2021

1044840611

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5036450

1 reference

1 reference

1 reference