(Q33749899)

29 July 2017

title

MPI-PHYLIP: parallelizing computationally intensive phylogenetic analysis routines for the analysis of large protein families (English)

1 reference

29 July 2017

1 reference

computational biology

1 reference

based on heuristic

inferred from title

author name string

Alexander J Ropelewski

series ordinal

1

1 reference

29 July 2017

Hugh B Nicholas

series ordinal

2

1 reference

29 July 2017

Ricardo R Gonzalez Mendez

series ordinal

3

1 reference

29 July 2017

language of work or name

English

0 references

publication date

15 November 2010

1 reference

29 July 2017

1 reference

29 July 2017

volume

5

1 reference

29 July 2017

issue

11

1 reference

29 July 2017

page(s)

e13999

1 reference

Creative Commons Attribution 4.0 International

29 July 2017

copyright license

start time

15 November 2010

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

Phylogenomic analysis of the cystatin superfamily in eukaryotes and prokaryotes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981553

A rapid bootstrap algorithm for the RAxML Web servers

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981553

Dynamics of genome rearrangement in bacterial populations

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981553

Determinants of protein function revealed by combinatorial entropy optimization

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981553

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981553

MultiPhyl: a high-throughput phylogenomics webserver using distributed computing

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981553

MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981553

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981553

Evolution of hormone-receptor complexity by molecular exploitation

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981553

Toward Automatic Reconstruction of a Highly Resolved Tree of Life

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981553

Diagnosing duplications--can it be done?

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981553

Phylogenomics and the reconstruction of the tree of life

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981553

Phylogeny determined by protein domain content

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981553

RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981553

DPRml: distributed phylogeny reconstruction by maximum likelihood.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981553

HyPhy: hypothesis testing using phylogenies

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981553

The ABC transporter gene family of Caenorhabditis elegans has implications for the evolutionary dynamics of multidrug resistance in eukaryotes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981553

Parallel Metropolis coupled Markov chain Monte Carlo for Bayesian phylogenetic inference

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981553

The challenge of constructing large phylogenetic trees

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981553

TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981553

Theory and practice of parallel direct optimization.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981553

Relationships within the aldehyde dehydrogenase extended family

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981553

Efficiencies of different genes and different tree-building methods in recovering a known vertebrate phylogeny.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981553

A Hidden Markov Model approach to variation among sites in rate of evolution

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981553

fastDNAmL: a tool for construction of phylogenetic trees of DNA sequences using maximum likelihood.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981553

The number of replications needed for accurate estimation of the bootstrap P value in phylogenetic studies

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981553

Comparison of Bayesian and maximum likelihood bootstrap measures of phylogenetic reliability.

21 June 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0013999

A hybrid micro-macroevolutionary approach to gene tree reconstruction.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0013999

pIQPNNI: parallel reconstruction of large maximum likelihood phylogenies.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0013999

An algorithm for identification and ranking of family-specific residues, applied to the ALDH3 family

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0013999

Initial catalytic events in class 3 aldehyde dehydrogenase: MM and QM/MM simulations

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0013999

INTREPID--INformation-theoretic TREe traversal for Protein functional site IDentification

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0013999

AxML: a fast program for sequential and parallel phylogenetic tree calculations based on the maximum likelihood method.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981553

ClustalW-MPI: ClustalW analysis using distributed and parallel computing

30 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21085574

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PONE.0013999

1 reference

29 July 2017

0 references

1 reference

29 July 2017

1 reference