Multiple sequence alignment: a major challenge to large-scale phylogenetics (Q33757469)

29 July 2017

Multiple sequence alignment: a major challenge to large-scale phylogenetics (English)

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29 July 2017

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3

Tandy Warnow

1 reference

29 July 2017

2

C Randal Linder

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29 July 2017

Kevin Liu

1

1 reference

29 July 2017

19 November 2010

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29 July 2017

1 reference

29 July 2017

2

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29 July 2017

RRN1198

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The impact of multiple protein sequence alignment on phylogenetic estimation

29 July 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2989897

Fast statistical alignment

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2989897

FastTree: computing large minimum evolution trees with profiles instead of a distance matrix

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2989897

A rapid bootstrap algorithm for the RAxML Web servers

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2989897

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2989897

Recent developments in the MAFFT multiple sequence alignment program

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2989897

Probalign: multiple sequence alignment using partition function posterior probabilities

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2989897

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2989897

Exploring the relationship between sequence similarity and accurate phylogenetic trees.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2989897

Joint Bayesian Estimation of Alignment and Phylogeny

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2989897

An algorithm for progressive multiple alignment of sequences with insertions

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2989897

ProbCons: Probabilistic consistency-based multiple sequence alignment

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2989897

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2989897

The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2989897

A comprehensive comparison of multiple sequence alignment programs

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2989897

Effects of nucleotide sequence alignment on phylogeny estimation: a case study of 18S rDNAs of apicomplexa

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2989897

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2989897

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2989897

Rapid and accurate large-scale coestimation of sequence alignments and phylogenetic trees

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2989897

The effect of the guide tree on multiple sequence alignments and subsequent phylogenetic analyses.

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2989897

Multiple alignment by aligning alignments.

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2989897

PartTree: an algorithm to build an approximate tree from a large number of unaligned sequences

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2989897

Comparison of the accuracies of several phylogenetic methods using protein and DNA sequences.

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2989897

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

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2989897

Barking up the wrong treelength: the impact of gap penalty on alignment and tree accuracy

30 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21113338

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

SATCHMO: sequence alignment and tree construction using hidden Markov models

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21113338

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Multiple Sequence Alignment Accuracy and Phylogenetic Inference

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21113338

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/CURRENTS.RRN1198

0 references

PMCID

2989897

1 reference

29 July 2017

1 reference

PubMed ID

21113338