Bioinformatics (Oxford, England) (Bioinformatics)

Journal PubWeight™ 17544.63‹?›

Top papers

Rank Title Year PubWeight™‹?›
1 The Sequence Alignment/Map format and SAMtools. 2009 232.39
2 Fast and accurate short read alignment with Burrows-Wheeler transform. 2009 190.94
3 MrBayes 3: Bayesian phylogenetic inference under mixed models. 2003 130.85
4 Clustal W and Clustal X version 2.0. 2007 126.47
5 Haploview: analysis and visualization of LD and haplotype maps. 2004 125.23
6 MRBAYES: Bayesian inference of phylogenetic trees. 2001 101.31
7 MODELTEST: testing the model of DNA substitution. 1998 101.19
8 RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. 2006 87.59
9 A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. 2003 82.89
10 TopHat: discovering splice junctions with RNA-Seq. 2009 81.13
11 SOAP: short oligonucleotide alignment program. 2008 68.13
12 edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. 2009 67.17
13 GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research--an update. 2012 65.14
14 Profile hidden Markov models. 1998 56.04
15 BEDTools: a flexible suite of utilities for comparing genomic features. 2010 53.23
16 Fast and accurate long-read alignment with Burrows-Wheeler transform. 2010 52.01
17 Search and clustering orders of magnitude faster than BLAST. 2010 51.97
18 Identifying bacterial genes and endosymbiont DNA with Glimmer. 2007 47.63
19 Artemis: sequence visualization and annotation. 2000 46.68
20 Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. 2005 46.40
21 DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. 2009 44.48
22 Trimmomatic: a flexible trimmer for Illumina sequence data. 2014 44.23
23 Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. 2006 43.68
24 SOAP2: an improved ultrafast tool for short read alignment. 2009 39.47
25 APE: Analyses of Phylogenetics and Evolution in R language. 2004 39.31
26 MEGA2: molecular evolutionary genetics analysis software. 2001 38.50
27 PatternHunter: faster and more sensitive homology search. 2002 35.65
28 The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling. 2005 34.83
29 Generating samples under a Wright-Fisher neutral model of genetic variation. 2002 34.50
30 A novel method for automatic functional annotation of proteins. 1999 33.88
31 The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. 2003 32.92
32 Prokka: rapid prokaryotic genome annotation. 2014 32.73
33 DnaSP, DNA polymorphism analyses by the coalescent and other methods. 2003 32.63
34 affy--analysis of Affymetrix GeneChip data at the probe level. 2004 32.08
35 Jalview Version 2--a multiple sequence alignment editor and analysis workbench. 2009 31.84
36 GOstat: find statistically overrepresented Gene Ontologies within a group of genes. 2004 30.14
37 ZOOM! Zillions of oligos mapped. 2008 29.78
38 UCHIME improves sensitivity and speed of chimera detection. 2011 29.22
39 InterProScan--an integration platform for the signature-recognition methods in InterPro. 2001 28.35
40 RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. 2014 28.04
41 Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. 2012 26.90
42 Cytoscape 2.8: new features for data integration and network visualization. 2010 26.76
43 FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes. 2004 26.64
44 The variant call format and VCFtools. 2011 25.88
45 Compressed indexing and local alignment of DNA. 2008 25.28
46 STAR: ultrafast universal RNA-seq aligner. 2012 25.21
47 SeqMap: mapping massive amount of oligonucleotides to the genome. 2008 24.32
48 Java Treeview--extensible visualization of microarray data. 2004 24.12
49 BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks. 2005 24.04
50 Scaffolding pre-assembled contigs using SSPACE. 2010 23.27
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