Related references
Note: Only part of the references are listed.Parametric and non-parametric masking of randomness in sequence alignments can be improved and leads to better resolved trees
Patrick Kueck et al.
FRONTIERS IN ZOOLOGY (2010)
An Alignment Confidence Score Capturing Robustness to Guide Tree Uncertainty
Osnat Penn et al.
MOLECULAR BIOLOGY AND EVOLUTION (2010)
Phylogenetic assessment of alignments reveals neglected tree signal in gaps
Christophe Dessimoz et al.
GENOME BIOLOGY (2010)
A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea
Dongying Wu et al.
NATURE (2009)
Rapid and Accurate Large-Scale Coestimation of Sequence Alignments and Phylogenetic Trees
Kevin Liu et al.
SCIENCE (2009)
Fast Statistical Alignment
Robert K. Bradley et al.
PLOS COMPUTATIONAL BIOLOGY (2009)
Using ESTs for phylogenomics: Can one accurately infer a phylogenetic tree from a gappy alignment?
Stefanie Hartmann et al.
BMC EVOLUTIONARY BIOLOGY (2008)
Alignment uncertainty and genomic analysis
Karen M. Wong et al.
SCIENCE (2008)
Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis
Ari Loytynoja et al.
SCIENCE (2008)
A simple, fast, and accurate method of phylogenomic inference
Martin Wu et al.
GENOME BIOLOGY (2008)
Heads or tails: A simple reliability check for multiple sequence alignments
Giddy Landan et al.
MOLECULAR BIOLOGY AND EVOLUTION (2007)
Multiple alignment by sequence annealing
Ariel S. Schwartz et al.
BIOINFORMATICS (2007)
Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments
Gerard Talavera et al.
SYSTEMATIC BIOLOGY (2007)
Probalign: multiple sequence alignment using partition function posterior probabilities
Usman Roshan et al.
BIOINFORMATICS (2006)
RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
Alexandros Stamatakis
BIOINFORMATICS (2006)
MUMMALS: multiple sequence alignment improved by using hidden Markov models with local structural information
Jimin Pei et al.
NUCLEIC ACIDS RESEARCH (2006)
Multiple sequence alignment accuracy and phylogenetic inference
TH Ogden et al.
SYSTEMATIC BIOLOGY (2006)
Multiple sequence alignment
Robert C. Edgar et al.
CURRENT OPINION IN STRUCTURAL BIOLOGY (2006)
Phylogenetic diversity and the greedy algorithm
M Steel
SYSTEMATIC BIOLOGY (2005)
Joint Bayesian estimation of alignment and phylogeny
BD Redelings et al.
SYSTEMATIC BIOLOGY (2005)
Evolutionary distance estimation and fidelity of pair wise sequence alignment
MS Rosenberg
BMC BIOINFORMATICS (2005)
SABmark - a benchmark for sequence alignment that covers the entire known fold space
I Van Walle et al.
BIOINFORMATICS (2005)
Comparison of the accuracies of several phylogenetic methods using protein and DNA sequences
BG Hall
MOLECULAR BIOLOGY AND EVOLUTION (2005)
ProbCons: Probabilistic consistency-based multiple sequence alignment
CB Do et al.
GENOME RESEARCH (2005)
Automatic assessment of alignment quality
T Lassmann et al.
NUCLEIC ACIDS RESEARCH (2005)
MUSCLE: multiple sequence alignment with high accuracy and high throughput
RC Edgar
NUCLEIC ACIDS RESEARCH (2004)
A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood
S Guindon et al.
SYSTEMATIC BIOLOGY (2003)
AVID: A global alignment program
N Bray et al.
GENOME RESEARCH (2003)
Quality assessment of multiple alignment programs
T Lassmann et al.
FEBS LETTERS (2002)
MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform
K Katoh et al.
NUCLEIC ACIDS RESEARCH (2002)
PAL: an object-oriented programming library for molecular evolution and phylogenetics
A Drummond et al.
BIOINFORMATICS (2001)
SOAP, cleaning multiple alignments from unstable blocks
A Löytynoja et al.
BIOINFORMATICS (2001)
T-Coffee: A novel method for fast and accurate multiple sequence alignment
C Notredame et al.
JOURNAL OF MOLECULAR BIOLOGY (2000)
Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis
J Castresana
MOLECULAR BIOLOGY AND EVOLUTION (2000)