Published in Genome Biol on April 06, 2010
MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol (2013) 34.34
Survey of branch support methods demonstrates accuracy, power, and robustness of fast likelihood-based approximation schemes. Syst Biol (2011) 2.66
Accurate extension of multiple sequence alignments using a phylogeny-aware graph algorithm. Bioinformatics (2012) 2.07
Issues in bioinformatics benchmarking: the case study of multiple sequence alignment. Nucleic Acids Res (2010) 2.05
webPRANK: a phylogeny-aware multiple sequence aligner with interactive alignment browser. BMC Bioinformatics (2010) 1.99
A comprehensive benchmark study of multiple sequence alignment methods: current challenges and future perspectives. PLoS One (2011) 1.65
CodonPhyML: fast maximum likelihood phylogeny estimation under codon substitution models. Mol Biol Evol (2013) 1.37
Accounting for alignment uncertainty in phylogenomics. PLoS One (2012) 1.35
Simple chained guide trees give poorer multiple sequence alignments than inferred trees in simulation and phylogenetic benchmarks. Proc Natl Acad Sci U S A (2015) 0.99
Species discrimination and phylogenetic inference of 17 Chinese Leishmania isolates based on internal transcribed spacer 1 (ITS1) sequences. Parasitol Res (2010) 0.99
Current Methods for Automated Filtering of Multiple Sequence Alignments Frequently Worsen Single-Gene Phylogenetic Inference. Syst Biol (2015) 0.94
Re-mind the gap! Insertion - deletion data reveal neglected phylogenetic potential of the nuclear ribosomal internal transcribed spacer (ITS) of fungi. PLoS One (2012) 0.87
Measuring guide-tree dependency of inferred gaps in progressive aligners. Bioinformatics (2013) 0.87
A classification of bioinformatics algorithms from the viewpoint of maximizing expected accuracy (MEA). J Comput Biol (2012) 0.85
Diversity measures in environmental sequences are highly dependent on alignment quality--data from ITS and new LSU primers targeting basidiomycetes. PLoS One (2012) 0.83
DendroBLAST: approximate phylogenetic trees in the absence of multiple sequence alignments. PLoS One (2013) 0.81
Proving universal common ancestry with similar sequences. Trends Evol Biol (2012) 0.81
Efficient representation of uncertainty in multiple sequence alignments using directed acyclic graphs. BMC Bioinformatics (2015) 0.81
Expanding the Halohydrin Dehalogenase Enzyme Family: Identification of Novel Enzymes by Database Mining. Appl Environ Microbiol (2014) 0.81
Fast and robust multiple sequence alignment with phylogeny-aware gap placement. BMC Bioinformatics (2012) 0.81
Relationships of wild and domesticated rices (Oryza AA genome species) based upon whole chloroplast genome sequences. Sci Rep (2015) 0.80
Inferring Orthologs: Open Questions and Perspectives. Genomics Insights (2016) 0.79
Surprising results on phylogenetic tree building methods based on molecular sequences. BMC Bioinformatics (2012) 0.79
Simultaneous Bayesian estimation of alignment and phylogeny under a joint model of protein sequence and structure. Mol Biol Evol (2014) 0.78
Mean protein evolutionary distance: a method for comparative protein evolution and its application. PLoS One (2013) 0.77
A phylogenetic analysis of normal modes evolution in enzymes and its relationship to enzyme function. J Mol Biol (2012) 0.76
A window into domain amplification through Piccolo in teleost fish. G3 (Bethesda) (2012) 0.76
Protein Multiple Sequence Alignment Benchmarking through Secondary Structure Prediction. Bioinformatics (2017) 0.75
ALVIS: interactive non-aggregative visualization and explorative analysis of multiple sequence alignments. Nucleic Acids Res (2016) 0.75
dCITE: Measuring Necessary Cladistic Information Can Help You Reduce Polytomy Artefacts in Trees. PLoS One (2016) 0.75
Evolutionary genomics and adaptive evolution of the Hedgehog gene family (Shh, Ihh and Dhh) in vertebrates. PLoS One (2014) 0.75
Maximum Likelihood Phylogenetic Inference is Consistent on Multiple Sequence Alignments, with or without Gaps. Syst Biol (2015) 0.75
Phylogenetic study of Class Armophorea (Alveolata, Ciliophora) based on 18S-rDNA data. Genet Mol Biol (2013) 0.75
Clustal W and Clustal X version 2.0. Bioinformatics (2007) 126.47
A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol (2003) 102.57
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics (2006) 87.59
T-Coffee: A novel method for fast and accurate multiple sequence alignment. J Mol Biol (2000) 57.88
MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics (2004) 50.89
MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res (2005) 31.64
Distinguishing homologous from analogous proteins. Syst Zool (1970) 25.10
Recent developments in the MAFFT multiple sequence alignment program. Brief Bioinform (2008) 22.07
The relation between the divergence of sequence and structure in proteins. EMBO J (1986) 16.66
Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst Biol (2007) 14.96
DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment. Bioinformatics (1999) 12.22
ProbCons: Probabilistic consistency-based multiple sequence alignment. Genome Res (2005) 11.90
Exhaustive matching of the entire protein sequence database. Science (1992) 11.29
Kalign--an accurate and fast multiple sequence alignment algorithm. BMC Bioinformatics (2005) 7.01
BAliBASE 3.0: latest developments of the multiple sequence alignment benchmark. Proteins (2005) 6.57
Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis. Science (2008) 6.35
An algorithm for progressive multiple alignment of sequences with insertions. Proc Natl Acad Sci U S A (2005) 6.26
Recent evolutions of multiple sequence alignment algorithms. PLoS Comput Biol (2007) 4.88
Phylogenetic and functional assessment of orthologs inference projects and methods. PLoS Comput Biol (2009) 4.65
Alignment uncertainty and genomic analysis. Science (2008) 4.09
Rapid and accurate large-scale coestimation of sequence alignments and phylogenetic trees. Science (2009) 3.82
Multiple rounds of speciation associated with reciprocal gene loss in polyploid yeasts. Nature (2006) 3.39
SABmark--a benchmark for sequence alignment that covers the entire known fold space. Bioinformatics (2004) 3.11
Multiple sequence alignment. Curr Opin Struct Biol (2006) 2.93
Upcoming challenges for multiple sequence alignment methods in the high-throughput era. Bioinformatics (2009) 2.64
The accuracy of several multiple sequence alignment programs for proteins. BMC Bioinformatics (2006) 2.52
Algorithm of OMA for large-scale orthology inference. BMC Bioinformatics (2008) 2.37
Analysis and comparison of benchmarks for multiple sequence alignment. In Silico Biol (2006) 2.33
Orthology prediction at scalable resolution by phylogenetic tree analysis. BMC Bioinformatics (2007) 2.29
HOMSTRAD: recent developments of the Homologous Protein Structure Alignment Database. Nucleic Acids Res (2004) 2.19
Darwin v. 2.0: an interpreted computer language for the biosciences. Bioinformatics (2000) 2.17
Probalign: multiple sequence alignment using partition function posterior probabilities. Bioinformatics (2006) 2.13
DIALIGN-TX: greedy and progressive approaches for segment-based multiple sequence alignment. Algorithms Mol Biol (2008) 2.07
Functional coverage of the human genome by existing structures, structural genomics targets, and homology models. PLoS Comput Biol (2005) 2.04
Automatic assessment of alignment quality. Nucleic Acids Res (2005) 1.97
Multiple sequence alignment: in pursuit of homologous DNA positions. Genome Res (2007) 1.92
DIALIGN-T: an improved algorithm for segment-based multiple sequence alignment. BMC Bioinformatics (2005) 1.87
MUMMALS: multiple sequence alignment improved by using hidden Markov models with local structural information. Nucleic Acids Res (2006) 1.85
Multiple sequence alignment accuracy and phylogenetic inference. Syst Biol (2006) 1.73
Multiple alignment by sequence annealing. Bioinformatics (2007) 1.63
Comparison of the accuracies of several phylogenetic methods using protein and DNA sequences. Mol Biol Evol (2004) 1.41
How should species phylogenies be inferred from sequence data? Syst Biol (1999) 1.37
The impact of multiple protein sequence alignment on phylogenetic estimation. IEEE/ACM Trans Comput Biol Bioinform (2011) 1.31
Biological sequence simulation for testing complex evolutionary hypotheses: indel-Seq-Gen version 2.0. Mol Biol Evol (2009) 1.23
Phylogenetic inference under varying proportions of indel-induced alignment gaps. BMC Evol Biol (2009) 1.17
Characterization of pairwise and multiple sequence alignment errors. Gene (2008) 1.11
Evolutionary distance estimation and fidelity of pair wise sequence alignment. BMC Bioinformatics (2005) 1.06
Exploring bias in the Protein Data Bank using contrast classifiers. Pac Symp Biocomput (2004) 1.00
SynPAM-a distance measure based on synonymous codon substitutions. IEEE/ACM Trans Comput Biol Bioinform (2007) 0.90
Survey of branch support methods demonstrates accuracy, power, and robustness of fast likelihood-based approximation schemes. Syst Biol (2011) 2.66
Beta-AMYLASE4, a noncatalytic protein required for starch breakdown, acts upstream of three active beta-amylases in Arabidopsis chloroplasts. Plant Cell (2008) 1.72
Inferring hierarchical orthologous groups from orthologous gene pairs. PLoS One (2013) 1.36
Who watches the watchmen? An appraisal of benchmarks for multiple sequence alignment. Methods Mol Biol (2014) 1.12
Fast estimation of the difference between two PAM/JTT evolutionary distances in triplets of homologous sequences. BMC Bioinformatics (2006) 0.92
Covariance of maximum likelihood evolutionary distances between sequences aligned pairwise. BMC Evol Biol (2008) 0.82
[Laparoscopic treatment of ventral hernia under spinal anesthesia]. Cir Esp (2006) 0.79
Chlamydia pneumoniae in the atherosclerotic plaques of patients with unstable angina undergoing coronary artery bypass grafting: does it have prognostic implications? Int J Cardiol (2003) 0.77
High prevalence and advanced silicosis in active granite workers: a dose-response analysis including FEV1. J Occup Environ Med (2008) 0.77