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Times Cited: 6898
Times Cited: 6898
Times Cited
Times Co-cited
Similarity
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BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs.
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Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments.
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Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation.
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Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement.
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Infernal 1.1: 100-fold faster RNA homology searches.
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Eric P Nawrocki, Sean R Eddy. Bioinformatics 2013
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S F Altschul, W Gish, W Miller, E W Myers, D J Lipman. J Mol Biol 1990
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OrthoMCL: identification of ortholog groups for eukaryotic genomes.
Li Li, Christian J Stoeckert, David S Roos. Genome Res 2003
Li Li, Christian J Stoeckert, David S Roos. Genome Res 2003
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RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies.
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LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons.
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MAFFT multiple sequence alignment software version 7: improvements in performance and usability.
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TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders.
W H Majoros, M Pertea, S L Salzberg. Bioinformatics 2004
W H Majoros, M Pertea, S L Salzberg. Bioinformatics 2004
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Fast and accurate short read alignment with Burrows-Wheeler transform.
Heng Li, Richard Durbin. Bioinformatics 2009
Heng Li, Richard Durbin. Bioinformatics 2009
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Using RepeatMasker to identify repetitive elements in genomic sequences.
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Prodigal: prokaryotic gene recognition and translation initiation site identification.
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Doug Hyatt, Gwo-Liang Chen, Philip F Locascio, Miriam L Land, Frank W Larimer, Loren J Hauser. BMC Bioinformatics 2010
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Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
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IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies.
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Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions.
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CAFE: a computational tool for the study of gene family evolution.
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Repbase Update, a database of eukaryotic repetitive elements.
J Jurka, V V Kapitonov, A Pavlicek, P Klonowski, O Kohany, J Walichiewicz. Cytogenet Genome Res 2005
J Jurka, V V Kapitonov, A Pavlicek, P Klonowski, O Kohany, J Walichiewicz. Cytogenet Genome Res 2005
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Rfam: annotating non-coding RNAs in complete genomes.
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Repbase Update, a database of repetitive elements in eukaryotic genomes.
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Versatile and open software for comparing large genomes.
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Stefan Kurtz, Adam Phillippy, Arthur L Delcher, Michael Smoot, Martin Shumway, Corina Antonescu, Steven L Salzberg. Genome Biol 2004
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De novo identification of repeat families in large genomes.
Alkes L Price, Neil C Jones, Pavel A Pevzner. Bioinformatics 2005
Alkes L Price, Neil C Jones, Pavel A Pevzner. Bioinformatics 2005
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Using intron position conservation for homology-based gene prediction.
Jens Keilwagen, Michael Wenk, Jessica L Erickson, Martin H Schattat, Jan Grau, Frank Hartung. Nucleic Acids Res 2016
Jens Keilwagen, Michael Wenk, Jessica L Erickson, Martin H Schattat, Jan Grau, Frank Hartung. Nucleic Acids Res 2016
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MUSCLE: multiple sequence alignment with high accuracy and high throughput.
Robert C Edgar. Nucleic Acids Res 2004
Robert C Edgar. Nucleic Acids Res 2004
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AUGUSTUS: ab initio prediction of alternative transcripts.
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HISAT: a fast spliced aligner with low memory requirements.
Daehwan Kim, Ben Langmead, Steven L Salzberg. Nat Methods 2015
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MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms.
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The Sequence Alignment/Map format and SAMtools.
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HiC-Pro: an optimized and flexible pipeline for Hi-C data processing.
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The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003.
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Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies.
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Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.
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Circos: an information aesthetic for comparative genomics.
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SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing.
Anton Bankevich, Sergey Nurk, Dmitry Antipov, Alexey A Gurevich, Mikhail Dvorkin, Alexander S Kulikov, Valery M Lesin, Sergey I Nikolenko, Son Pham, Andrey D Prjibelski,[...]. J Comput Biol 2012
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8
Co-cited is the co-citation frequency, indicating how many articles cite the article together with the query article. Similarity is the co-citation as percentage of the times cited of the query article or the article in the search results, whichever is the lowest. These numbers are calculated for the last 100 citations when articles are cited more than 100 times.