Search results

• Artemis
  Bioinformatics (Oxford, England) 2012;28;4;464-9 PUBMED: 22199388; PMC: 3278759; DOI: 10.1093/bioinformatics/btr703
  3 KB (378 words) - 14:53, 12 August 2022
• BESST
  ...vestad L (2012) "Improved gap size estimation for scaffolding algorithms." Bioinformatics 28(17), 2215-2222] ...(2014) "BESST--efficient scaffolding of large fragmented assemblies." BMC Bioinformatics 15, 281]
  3 KB (332 words) - 12:51, 15 August 2022
• Csvtk
  ...informatics, CSV/TSV formats are basic and ubiquitous file formats in both Bioinformatics and data science.
  2 KB (260 words) - 18:44, 12 August 2022
• Minimap2
  ...gnment for nucleotide sequences. Bioinformatics, 34:3094-3100. doi:10.1093/bioinformatics/bty191
  2 KB (260 words) - 13:31, 15 August 2022
• MultiQC
  ...QC is a tool to create a single report with interactive plots for multiple bioinformatics analyses across many samples. ...single report Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller Bioinformatics (2016)]
  2 KB (285 words) - 19:54, 12 August 2022
• Lambda
  ...Singer, Knut Reinert; Bioinformatics 2014 30 (17): i349-i355; doi: 10.1093/bioinformatics/btu439
  2 KB (279 words) - 21:21, 6 December 2019
• Newick utils
  ...ree Processing in the UNIX Shell. ''Thomas Junier and Evgeny M. Zdobnov''. Bioinformatics 2010 26:1669-1670 [http://bioinformatics.oxfordjournals.org/content/26/13/1669.full http://bioinformatics.oxfordjournals.org/content/26/13/1669.full]
  3 KB (305 words) - 14:10, 1 September 2021
• Bismark
  |{{#vardefine:url|http://www.bioinformatics.babraham.ac.uk/projects/download.html#bismark}} Bisulfite-Seq applications. Bioinformatics. 2011 Jun 1;27(11):1571-2. doi:
  2 KB (293 words) - 18:17, 12 August 2022
• STAR
  A. Dobin et al, Bioinformatics 2012; doi: 10.1093/bioinformatics/bts635 "STAR: ultrafast universal RNA-seq aligner"
  2 KB (291 words) - 16:01, 22 August 2022
• Mapdamage
  ...ncient DNA damage parameters. Bioinformatics 23rd April 2013. doi: 10.1093/bioinformatics/btt193]
  3 KB (299 words) - 21:28, 16 September 2022
• SortMeRNA
  ...omal RNAs in metatranscriptomic data", Bioinformatics (2012), doi: 10.1093/bioinformatics/bts611.]
  3 KB (299 words) - 17:00, 10 June 2022
• Tax4Fun
  ...enomic 16S rRNA data Bioinformatics (2015) 31 (17): 2882-2884. doi:10.1093/bioinformatics/btv287.]
  3 KB (303 words) - 18:29, 4 February 2020
• V-pipe
  ...rom high-throughput sequencing data." Bioinformatics, January. doi:10.1093/bioinformatics/btab015.
  3 KB (296 words) - 17:20, 22 August 2022
• NextGenMap
  ...013) 29 (21): 2790-2791 first published online August 23, 2013 doi:10.1093/bioinformatics/btt468]
  3 KB (309 words) - 16:24, 19 August 2022
• SeSiMCMC
  Bioinformatics. 2005 May 15;21(10):2240-5. doi: 10.1093/bioinformatics/bti336. Epub 2005 Feb 22.
  3 KB (299 words) - 22:41, 21 August 2022
• MELTING
  ...(2001). MELTING, computing the melting temperature of nucleic acid duplex. Bioinformatics, 17: 1226-1227. ...lexible platform to predict the melting temperatures of nucleic acids. BMC Bioinformatics, 13: 101.
  3 KB (306 words) - 19:50, 12 August 2022
• NtEdit
  ...n Bousquet, Joerg Bohlmann, Inanc Birol. 2019. Bioinformatics. doi:10.1093/bioinformatics/btz400]
  3 KB (316 words) - 21:23, 6 December 2019
• Circleator
  ...on of genome-associated data with BioPerl and SVG. Bioinformatics, 10.1093/bioinformatics/btu505.]
  3 KB (319 words) - 21:18, 6 December 2019
• IVA
  Bioinformatics. 2015 Jul 15;31(14):2374-6. doi: 10.1093/bioinformatics/btv120. Epub 2015 Feb 28.
  2 KB (300 words) - 16:06, 7 December 2021
• BAM-matcher
  ...ker; Susan Branford; Andreas W. Schreiber Bioinformatics 2016 doi: 10.1093/bioinformatics/btw239]
  3 KB (324 words) - 21:07, 6 December 2019
• BRM
  ...apping based on bulked segregant analysis by deep sequencing" published in Bioinformatics. ...hod for QTL mapping based on bulked segregant analysis by deep sequencing. Bioinformatics, 2019.]
  3 KB (320 words) - 21:54, 26 August 2020
• YAHA
  ...on. Bioinformatics (2012) 28(19): 2417-2424. Epub 2012 Jul 24. doi:10.1093/bioinformatics.
  3 KB (320 words) - 20:56, 12 August 2022
• RSeQC
  ...RNA-seq experiments Bioinformatics (2012) 28 (16): 2184-2185. doi: 10.1093/bioinformatics/bts356 pubmed]
  3 KB (328 words) - 17:48, 10 June 2022
• MaSuRCA
  ...A. et al. The MaSuRCA genome Assembler. Bioinformatics (2013). doi:10.1093/bioinformatics/btt476
  3 KB (340 words) - 18:24, 18 August 2022
• CANVAS
  ...ersatile and scalable detection of copy number variants in the journal OUP Bioinformatics] ...btx618 The Canvas Small Pedigree Workflow was published in the journal OUP Bioinformatics: Canvas SPW: calling de novo copy number variants in pedigrees]
  3 KB (342 words) - 22:23, 26 August 2020
• PLAST
  * Composition-based score adjustments as in Bioinformatics 21:902-911 ...) PLAST: parallel local alignment search tool for database comparison. BMC Bioinformatics, vol 10, no 329.
  3 KB (320 words) - 20:23, 12 August 2022
• Ksnp
  Bioinformatics 31: 2877-2878 doi: 10.1093/bioinformatics/btv271.
  3 KB (327 words) - 12:56, 15 August 2022
• USEARCH
  Bioinformatics, 2010 Publication : Bioinformatics
  4 KB (559 words) - 17:19, 22 August 2022
• Xwalk
  ...lizing Distances in Cross-linking Experiments. Bioinformatics, doi:10.1093/bioinformatics/btr348.
  3 KB (345 words) - 16:47, 28 February 2023
• Viralmsa
  ...sequence alignment of viral genomes." Bioinformatics. btaa743. doi:10.1093/bioinformatics/btaa743]
  3 KB (357 words) - 19:56, 27 May 2022
• Matlab add-ons
  Bioinformatics Toolbox Version 4.3 (R2013a)
  2 KB (206 words) - 14:11, 30 June 2017
• ATRAM
  ...bling loci across divergent taxa from next-generation sequencing data. BMC Bioinformatics 16:98 DOI 10.1186/s12859-015-0515-2}} <!--CITATION--> ...bling loci across divergent taxa from next-generation sequencing data. BMC Bioinformatics 16:98 DOI 10.1186/s12859-015-0515-2]
  3 KB (350 words) - 15:23, 12 August 2022
• MEGAHIT
  ...nomics assembly via succinct de Bruijn graph. Bioinformatics, doi: 10.1093/bioinformatics/btv033]
  3 KB (367 words) - 18:31, 18 August 2022
• HTSeq
  ...in print, online at [http://doi:10.1093/bioinformatics/btu638 doi:10.1093/bioinformatics/btu638].
  3 KB (411 words) - 19:05, 12 August 2022
• Pygenometracks
  ...ariate genomic data sets. Bioinformatics. 2020 Aug 3:btaa692. doi: 10.1093/bioinformatics/btaa692. Epub ahead of print. PMID: 32745185.
  3 KB (375 words) - 20:54, 18 May 2023
• ASTRAL
  ...tp://bioinformatics.oxfordjournals.org/cgi/content/full/btu462 doi:10.1093/bioinformatics/btu462].
  3 KB (415 words) - 15:08, 12 August 2022
• Clann
  Clann has been published in Bioinformatics in 2005 under the following title: ...Clann: investigating phylogenetic information through supertree analyses. Bioinformatics 21(3): 390-2.
  3 KB (438 words) - 18:30, 12 August 2022
• MMseqs2
  ...app for fast, interactive sequence searches. Bioinformatics, doi: 10.1093/bioinformatics/bty1057 (2019).]
  3 KB (413 words) - 20:22, 2 October 2023
• SCRATCH-1D
  ...ed SCRATCH suite of predictors developed by the Institute for Genomics and Bioinformatics (IGB) of the University of California, Irvine (UCI). Bioinformatics, vol 30 (18), 2592-2597
  3 KB (381 words) - 20:35, 12 August 2022
• Uproc
  ...es in terms of similarities to known protein families challenges classical bioinformatics. The ultrafast protein classification (UProC) toolbox implements a novel al ...Peter. '''UProC: tools for ultra-fast protein domain classification'''. ''Bioinformatics'', 2014
  3 KB (418 words) - 20:53, 12 August 2022
• SAMStat
  ...ing biases in next generation sequencing data." Bioinformatics doi:10.1093/bioinformatics/btq614 [PMID: 21088025]
  3 KB (429 words) - 20:34, 12 August 2022
• Gmap
  Bioinformatics 2005 21:1859-1875 Bioinformatics 2010 26:873-881
  3 KB (450 words) - 17:11, 15 August 2022
• MetaBCC-LR
  @article{10.1093/bioinformatics/btaa441, journal = {Bioinformatics},
  6 KB (774 words) - 14:28, 15 December 2022
• Ngstools
  ...generation sequencing data.Fumagalli M, Vieira FG, Linderoth T, Nielsen R. Bioinformatics. 2014 May 15;30(10):1486-7 ...t Generation Sequencing Data. Korneliussen T, Albrechtsen A, Nielsen R BMC Bioinformatics. 2014 Nov 25;15(1):356
  5 KB (708 words) - 15:31, 14 December 2022
• Fast-Plast
  ...Usadel. 2014. Trimmomatic: A flexible trimmer for Illumina Sequence Data. Bioinformatics, btu170. ...ck-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics, 27:764-770.
  4 KB (487 words) - 21:20, 6 December 2019
• Scalpel
  Bioinformatics pipeline for discovery of genetic variants from NGS reads.
  2 KB (239 words) - 22:07, 21 August 2022
• Staphb-toolkit
  The StaPH-B ToolKit is a Python library of commonly used bioinformatics tools that help to inform public health action.
  2 KB (248 words) - 19:54, 2 June 2022
• Hyb
  Hyb is a bioinformatics pipeline for analysis of CLASH (crosslinking, ligation and sequencing of hy
  2 KB (247 words) - 15:07, 10 June 2022
• PacBio
  SMRT® Analysis is PacBio's bioinformatics software suite for analyzing single molecule, real-time DNA sequencing data
  2 KB (250 words) - 20:10, 24 August 2022
• Krona
  Krona Tools is a set of scripts to create Krona charts from several Bioinformatics tools as well as from text and XML files.
  2 KB (254 words) - 19:29, 12 August 2022
• Orthograph
  ...ral.com/articles/10.1186/s12859-017-1529-8 Orthograph was published in BMC Bioinformatics (2017).]
  2 KB (261 words) - 18:00, 19 August 2022
• HALC
  The HALC paper is accepted for publication in BMC Bioinformatics!
  2 KB (265 words) - 21:20, 6 December 2019
• FLEA
  FLEA is a bioinformatics pipeline for analyzing longitudinal sequencing data from the Pacific Biosci
  2 KB (260 words) - 22:01, 27 August 2020
• Nextclade
  Hadfield et al., Nextstrain: real-time tracking of pathogen evolution , Bioinformatics (2018)
  2 KB (260 words) - 19:03, 12 January 2023
• GeneSeqer
  ...sensus spliced alignment of multiple ESTs matching the same genomic locus. Bioinformatics 20, 1157-1169.
  2 KB (257 words) - 18:58, 12 August 2022
• Nanolyse
  ...ume 34, Issue 15, 01 August 2018, Pages 2666–2669, https://doi.org/10.1093/bioinformatics/bty149
  2 KB (260 words) - 19:24, 7 September 2022
• JCVI
  Collection of Python libraries to parse bioinformatics files, or perform computation related to assembly, annotation, and comparat
  2 KB (265 words) - 14:30, 4 September 2020
• GenomeTools
  The GenomeTools genome analysis system is a free collection of bioinformatics tools (in the realm of genome informatics) combined into a single binary na
  2 KB (266 words) - 18:58, 12 August 2022
• TrimAl
  ...009.pdf Salvador Capella-Gutierrez; Jose M. Silla-Martinez; Toni Gabaldon. Bioinformatics 2009 25: 1972-1973.]
  2 KB (264 words) - 19:32, 24 August 2022
• VEP
  McLaren et. al. (doi:10.1093/bioinformatics/btq330)
  2 KB (270 words) - 17:28, 22 August 2022
• Wgd
  ...command line tools for the analysis of ancient whole genome duplications. Bioinformatics., bty915]
  2 KB (270 words) - 19:52, 27 May 2022
• Kalign
  Bioinformatics (2019) https://doi.org/10.1093/bioinformatics/btz795
  2 KB (265 words) - 19:28, 12 August 2022
• PRINSEQ
  A bioinformatics tool to PRe-process and show INformation of SEQuence data. The tool is writ
  2 KB (271 words) - 15:52, 10 June 2022
• Plotsr
  ...n multiple genomes, Bioinformatics, 2022; btac196, https://doi.org/10.1093/bioinformatics/btac196
  2 KB (271 words) - 20:00, 5 August 2022
• Graph annotation
  ...s/article/35/3/407/5055406 Dynamic compression schemes for graph coloring, Bioinformatics, 2018 by Harun Mustafa, Ingo Schilken, Mikhail Karasikov, Carsten Eickhoff,
  2 KB (276 words) - 21:20, 6 December 2019
• Faqcs
  |{{#vardefine:url|https://github.com/LANL-Bioinformatics/FaQCs}} ...Sequencing Data with FaQCs. [https://pubmed.ncbi.nlm.nih.gov/25408143/ BMC Bioinformatics. 2014 Nov 19;15]
  2 KB (268 words) - 17:48, 18 May 2023
• Vt
  ...R. Abecasis and Hyun Min Kang. Unified Representation of Genetic Variants. Bioinformatics (2015) 31(13): 2202-2204]
  2 KB (273 words) - 16:13, 10 June 2022
• Phylonet
  ...ge for analyzing and reconstructing reticulate evolutionary histories, BMC Bioinformatics 9:322.
  2 KB (263 words) - 21:23, 6 December 2019
• Deepsig
  ...o R. DeepSig: deep learning improves signal peptide detection in proteins, Bioinformatics (2018) 34(10): 1690-1696.
  2 KB (266 words) - 04:24, 6 December 2022
• NxTrim
  ...l, Jared, et al. "NxTrim: optimized trimming of Illumina mate pair reads." Bioinformatics 31.12 (2015): 2035-2037.]
  2 KB (273 words) - 20:08, 12 August 2022
• Harvesttools
  ...ngr, HarvestTools can also be used for generic conversion between standard bioinformatics file formats.
  2 KB (285 words) - 17:38, 13 October 2022
• Miniwdl
  [[Category:Software]][[Category:Bioinformatics]]
  2 KB (283 words) - 18:55, 1 December 2023
• Phanotate
  ...e 35, Issue 22, 15 November 2019, Pages 4537–4542, https://doi.org/10.1093/bioinformatics/btz265
  2 KB (273 words) - 20:02, 8 November 2022
• Tiara
  ...Tiara: deep learning-based classification system for eukaryotic sequences, Bioinformatics, Volume 38, Issue 2, 15 January 2022, Pages 344–350]
  2 KB (272 words) - 16:36, 22 August 2022
• SEQPower
  |{{#vardefine:url|http://www.bioinformatics.org/spower}} ...nalysis and sample size estimation for sequence-based association studies. Bioinformatics. (2014)]
  2 KB (274 words) - 22:38, 21 August 2022
• GraphViz
  ...abstract graphs and networks. It has important applications in networking, bioinformatics, software engineering, database and web design, machine learning, and in v
  2 KB (276 words) - 19:03, 12 August 2022
• C-wap
  C-WAP is a bash-based bioinformatics pipeline for the analysis of either long-read (ONT or PacBio) or short-read
  2 KB (281 words) - 13:16, 15 August 2022
• Kmerdb
  ...t, M., Danek, A. (2019) Kmer-db: instant evolutionary distance estimation, Bioinformatics, 35(1): 133–136]
  2 KB (277 words) - 13:30, 15 August 2022
• SICER
  ...ng, Dustin E. Schones, Chen Zeng, Kairong Cui, Keji Zhao, and Weiqun Peng, Bioinformatics 25, 1952 - 1958 (2009)]
  2 KB (279 words) - 16:35, 10 June 2022
• Sate
  ...T. Holder. 2010. "DendroPy: A Python library for phylogenetic computing". Bioinformatics 26: 1569-1571. (for all SATé versions from this website) ...of the 15th ISCB Conference on Intelligent Systems for Molecular Biology, Bioinformatics'' '''23''', i559-i568, 2007. And see http://opal.cs.arizona.edu/
  7 KB (910 words) - 20:43, 21 December 2022
• Tapir
  Pond SLK, Frost SDW, Muse SV: HyPhy: hypothesis testing using phylogenies. Bioinformatics 2005, 21:676-679.
  2 KB (275 words) - 16:40, 10 June 2022
• Nubeamdedup
  nubeam-dedup is a fast and easy-to-use bioinformatics tool removing exact PCR duplicates for sequencing reads, single-end or pair [https://academic.oup.com/bioinformatics/article-abstract/36/10/3254/5753947?redirectedFrom=fulltext Hang Dai and Yo
  2 KB (282 words) - 17:23, 19 August 2022
• Circompara2
  ...e and robust circRNA detection from RNA-seq with CirComPara2, Briefings in Bioinformatics, 2021;, bbab418, https://doi.org/10.1093/bib/bbab418
  2 KB (283 words) - 21:36, 1 April 2022
• Rvtests
  ...prehensive Tool for Rare Variant Association Analysis Using Sequence Data. Bioinformatics 2016 32: 1423-1426.]
  3 KB (293 words) - 21:59, 21 August 2022
• Intervene
  ...ntersection and visualization of multiple gene or genomic region sets. BMC Bioinformatics. 2017;18:287. doi: 10.1186/s12859-017-1708-7]
  3 KB (295 words) - 21:21, 6 December 2019
• GramCluster
  BMC Bioinformatics 2010, 11:601
  2 KB (280 words) - 16:57, 10 June 2022
• SiLiX
  ...ntral.com/articles/10.1186/1471-2105-12-116 Miele V, Penel S, Duret L. BMC Bioinformatics. 2011 Apr 22;12:116. doi: 10.1186/1471-2105-12-116.]
  3 KB (287 words) - 21:24, 6 December 2019
• Kma
  ...precise alignment of raw reads against redundant databases with KMA", BMC Bioinformatics, 2018;19:307.
  2 KB (292 words) - 15:51, 30 January 2023
• Pseudofinder
  Pseudofinder is a bioinformatics tool that detects pseudogene candidates from annotated genbank files of bac
  3 KB (304 words) - 13:41, 11 October 2021
• Mccortex
  ...nformation into de Bruijn graphs Turner I, Garimella K, Iqbal Z, McVean G (Bioinformatics) (Advanced access 15 March 2018)]
  3 KB (297 words) - 22:22, 8 September 2020
• Nextstrain
  ...388 Hadfield et al., Nextstrain: real-time tracking of pathogen evolution, Bioinformatics (2018)]
  3 KB (295 words) - 14:56, 2 March 2020
• PHYUTILITY
  ...tility: a phyloinformatics tool for trees, alignments, and molecular data. Bioinformatics. 24: 715-716
  2 KB (296 words) - 20:22, 12 August 2022
• BRANCH
  |{{#vardefine:url|http://manuals.bioinformatics.ucr.edu/home/branch}} ...matics: [http://bioinformatics.oxfordjournals.org/content/early/2013/03/14/bioinformatics.btt127.abstract epub].
  3 KB (309 words) - 13:09, 15 August 2022
• Mugsy
  ...zberg SL. Mugsy: Fast multiple alignment of closely related whole genomes. Bioinformatics 2011 27(3):334-4]
  3 KB (298 words) - 21:22, 6 December 2019
• IAssembler
  ...kage for de novo assembly of Roche-454/Sanger transcriptome sequences. BMC Bioinformatics 12:453]
  3 KB (301 words) - 18:39, 15 August 2022
• VIRULIGN
  ...notation of viral genomes, Bioinformatics, bty851, https://doi.org/10.1093/bioinformatics/bty851]
  3 KB (304 words) - 19:53, 20 April 2020
• DeconSeq
  ...and Edwards R: Quality control and preprocessing of metagenomic datasets. Bioinformatics 2011, 27:863-864.]
  3 KB (299 words) - 17:00, 10 June 2022
• Synima
  ...biomedcentral.com/articles/10.1186/s12859-017-1939-7 Farrer RA (2017), BMC Bioinformatics 18:507]
  3 KB (313 words) - 20:34, 27 May 2022
• Recycler
  journal={Bioinformatics},
  3 KB (297 words) - 14:21, 11 October 2022
• Svim-asm
  ...free to read and cite our paper in Bioinformatics: https://doi.org/10.1093/bioinformatics/btaa1034
  3 KB (306 words) - 17:16, 31 May 2022

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