TCS: a new multiple sequence alignment reliability measure to estimate alignment accuracy and improve phylogenetic tree reconstruction (Q28237309)

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU117

Class of multiple sequence alignment algorithm affects genomic analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU117

Supertree bootstrapping methods for assessing phylogenetic variation among genes in genome-scale data sets

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU117

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU117

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU117

CaspR: a web server for automated molecular replacement using homology modelling

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU117

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU117

Theoretical foundation of the balanced minimum evolution method of phylogenetic inference and its relationship to weighted least-squares tree fitting

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU117

ProbCons: Probabilistic consistency-based multiple sequence alignment

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU117

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU117

MUSCLE: multiple sequence alignment with high accuracy and high throughput

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU117

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU117

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU117

Using ESTs for phylogenomics: can one accurately infer a phylogenetic tree from a gappy alignment?

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU117

MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU117

Recent developments in the MAFFT multiple sequence alignment program

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU117

Upcoming challenges for multiple sequence alignment methods in the high-throughput era

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU117

STRIKE: evaluation of protein MSAs using a single 3D structure

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU117

PSAR: measuring multiple sequence alignment reliability by probabilistic sampling.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU117

Clustal W and Clustal X version 2.0

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU117

Kalign--an accurate and fast multiple sequence alignment algorithm

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU117

A tool for multiple sequence alignment

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU117

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU117

SATe-II: very fast and accurate simultaneous estimation of multiple sequence alignments and phylogenetic trees.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU117

MSAProbs: multiple sequence alignment based on pair hidden Markov models and partition function posterior probabilities.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU117

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU117

A general method applicable to the search for similarities in the amino acid sequence of two proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU117

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU117

COFFEE: an objective function for multiple sequence alignments

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU117

An alignment confidence score capturing robustness to guide tree uncertainty

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU117

Genome-scale phylogeny and the detection of systematic biases

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU117

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU117

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU117

An empirical examination of the utility of codon-substitution models in phylogeny reconstruction

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU117

Genome-scale approaches to resolving incongruence in molecular phylogenies

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU117

Probalign: multiple sequence alignment using partition function posterior probabilities

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU117

Twilight zone of protein sequence alignments

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU117

Database of homology-derived protein structures and the structural meaning of sequence alignment

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU117

ROCR: visualizing classifier performance in R

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU117

Rose: generating sequence families.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU117

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU117

An assessment of accuracy, error, and conflict with support values from genome-scale phylogenetic data

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU117

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU117

On the complexity of multiple sequence alignment

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU117

Alignment uncertainty and genomic analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU117