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Found 273 Software Packages (Results 1–100)

BLAST

Software Authors:   Stephen F. Altschul, Thomas L. Madden, Alejandro A. Schäffer, Jinghui Zhang, Zheng Zhang, Webb Miller, David J. Lipman
Referenced in: 150 Publications (1999–2022)
Related Software: PSI-BLAST; Pfam; UniProt; ClustalW; MUSCLE; LIBSVM; …
Main Fields: Combinatorics (05-XX); Statistics (62-XX); Computer science (68-XX)

ClustalW

Software Authors:   J. Thompson-Maaloum, D. Higgins, T. Gibson
Referenced in: 99 Publications (1996–2022)
Related Software: MUSCLE; MAFFT; BLAST; T-coffee; PSI-BLAST; DIALIGN; …
Main Fields: Combinatorics (05-XX); Statistics (62-XX); Computer science (68-XX)

MUSCLE

Software Authors:   R.C. Edgar
Referenced in: 49 Publications (2005–2022)
Related Software: ClustalW; MAFFT; T-coffee; BLAST; PSI-BLAST; DIALIGN; …
Main Fields: Probability theory and stochastic processes (60-XX); Statistics (62-XX); Computer science (68-XX)

BWA

Software Authors:   Li H.; Durbin R.
Referenced in: 48 Publications (2010–2022)
Related Software: Soap; Bowtie 2; Samtools; PatternHunter; SHRiMP; GATK; …
Main Fields: Combinatorics (05-XX); Statistics (62-XX); Computer science (68-XX)

MAFFT

Software Authors:   Katoh K., Misawa K., Kuma K., Miyata T.
Referenced in: 26 Publications (2005–2021)
Related Software: MUSCLE; ClustalW; T-coffee; ProbCons; DIALIGN; Clustal X; …
Main Fields: Probability theory and stochastic processes (60-XX); Statistics (62-XX); Computer science (68-XX)

T-coffee

Software Authors:   C. Notredame, D.G. Higgins, J. Heringa
Referenced in: 30 Publications (2004–2022)
Related Software: ClustalW; MUSCLE; MAFFT; DIALIGN; ProbCons; Balibase; …
Main Fields: General and overarching topics; collections (00-XX); Statistics (62-XX); Computer science (68-XX)

MUMMER

Software Authors:   S. Kurtz, A. Phillippy, A.L. Delcher, M. Smoot, M. Shumway, C. Antonescu, S.L. Salzberg
Referenced in: 29 Publications (2003–2022)
Related Software: LAGAN; REPuter; BLASTZ; PatternHunter; AVID; DIALIGN; …
Main Fields: General and overarching topics; collections (00-XX); Combinatorics (05-XX); Computer science (68-XX)

Soap

Software Authors:   Ruiqiang Li; Yingrui Li; Karsten Kristiansen; Jun Wang
Referenced in: 26 Publications (2010–2021)
Related Software: BWA; Samtools; BLAT; R; SSAHA; PatternHunter; …
Main Fields: General and overarching topics; collections (00-XX); Statistics (62-XX); Computer science (68-XX)

BLAT

Software Authors:   W. James Kent
Referenced in: 21 Publications (2005–2018)
Related Software: Soap; PatternHunter; PSI-BLAST; BLAST; BLASTZ; AVID; …
Main Fields: General and overarching topics; collections (00-XX); Probability theory and stochastic processes (60-XX); Statistics (62-XX)

DIALIGN

Software Authors:   B. Morgenstern
Referenced in: 23 Publications (2001–2022)
Related Software: ClustalW; MUSCLE; T-coffee; MAFFT; ProbCons; Balibase; …
Main Fields: General and overarching topics; collections (00-XX); Statistics (62-XX); Computer science (68-XX)

MODELLER

Software Authors:   Andrej Šali et.al.
Referenced in: 19 Publications (2005–2021)
Related Software: BLAST; PSI-BLAST; PROCHECK; SWISS-MODEL; I-TASSER; PSIPRED; …
Main Fields: Combinatorics (05-XX); Several complex variables and analytic spaces (32-XX); Statistics (62-XX)

Clustal X

Software Authors:   Larkin, M. A.; Blackshields, G.; Brown, N.; Chenna, R.; Mcgettigan, P. A.; Mcwilliam, H.; Valentin, F.; Wallace, I. M.; Wilm, A.; Lopez, R.
Referenced in: 23 Publications (2006–2021)
Related Software: ClustalW; MUSCLE; MAFFT; T-coffee; DIALIGN; ProbCons; …
Main Fields: General and overarching topics; collections (00-XX); Probability theory and stochastic processes (60-XX); Statistics (62-XX)

WebLogo

Software Authors:   G.E. Crooks, G. Hon, J.-M. Chandonia, S.E. Brenner
Referenced in: 13 Publications (2004–2021)
Related Software: TRANSFAC; BioProspector; R; RegulonDB; LIBSVM; JASPAR; …
Main Fields: Statistics (62-XX); Computer science (68-XX); Operations research, mathematical programming (90-XX)

TopHat

Software Authors:   Kim D, Pertea G, Trapnell C et al
Referenced in: 20 Publications (2011–2021)
Related Software: Bioconductor; edgeR; R; KEGG; STAR; RSEM; …
Main Fields: General and overarching topics; collections (00-XX); Probability theory and stochastic processes (60-XX); Statistics (62-XX)

HMMER

Software Authors:   Robert D. Finn, Jody Clements, Sean R. Eddy
Referenced in: 12 Publications (2006–2019)
Related Software: ClustalW; UniProt; MUSCLE; MAFFT; R; MrBayes; …
Main Fields: General and overarching topics; collections (00-XX); Harmonic analysis on Euclidean spaces (42-XX); Statistics (62-XX)

CLUSTAL

Software Authors:   Higgins, D. G.; Sharp, P. M.
Referenced in: 14 Publications (1992–2017)
Related Software: ClustalW; MUSCLE; T-coffee; MAFFT; DIALIGN; Balibase; …
Main Fields: Probability theory and stochastic processes (60-XX); Computer science (68-XX); Operations research, mathematical programming (90-XX)

Mauve

Software Authors:   Darling AC, Mau B, Blattner FR, Perna NT
Referenced in: 11 Publications (2008–2022)
Related Software: OXBench; LAGAN; ClustalW; T-coffee; BLASTZ; BLAT; …
Main Fields: General and overarching topics; collections (00-XX); Combinatorics (05-XX); Statistics (62-XX)

IsoRank

Software Authors:   Rohit Singh, Jinbo Xu, Bonnie Berger
Referenced in: 12 Publications (2013–2022)
Related Software: IsoRankN; GHOST; Natalie; DeepWalk; node2vec; word2vec; …
Main Fields: Combinatorics (05-XX); Probability theory and stochastic processes (60-XX); Operations research, mathematical programming (90-XX)

ProbCons

Software Authors:   Chuong B. Do; Mahathi S.P. Mahabhashyam; Michael Brudno; Serafim Batzoglou
Referenced in: 9 Publications (2008–2021)
Related Software: MUSCLE; MAFFT; ClustalW; T-coffee; DIALIGN; Probalign; …
Main Fields: History and biography (01-XX); Statistics (62-XX); Computer science (68-XX)

Signal-3L

Software Authors:   Shen, H.B.; Chou, K.C.
Referenced in: 15 Publications (2009–2020)
Related Software: Signal-CF; Cell-PLoc; Memtype-2L; EzyPred; ProtIdent; Euk-mPLoc; …
Main Fields: Mathematical logic and foundations (03-XX); Combinatorics (05-XX); Statistics (62-XX)

TM-align

Software Authors:   Zhang, Y., Skolnick, J.
Referenced in: 9 Publications (2009–2021)
Related Software: BLAST; PSI-BLAST; ClustalW; MAMMOTH; SSAP; Gephi; …
Main Fields: Statistics (62-XX); Computer science (68-XX); Operations research, mathematical programming (90-XX)

ExPASy

Software Authors:   Gasteiger, E.; Gattiker, A.; Hoogland, C.; Ivanyi, I.; Appel, R. D.; Bairoch, A
Referenced in: 10 Publications (2006–2020)
Related Software: MODELLER; BLAST; PSI-BLAST; R; UniProt; PROCHECK; …
Main Fields: Statistics (62-XX); Computer science (68-XX); Biology and other natural sciences (92-XX)

Kalign

Software Authors:   T. Lassmann, O. Frings, E. Sonnhammer
Referenced in: 11 Publications (2011–2019)
Related Software: MUSCLE; ClustalW; T-coffee; MAFFT; ProbCons; Balibase; …
Main Fields: General and overarching topics; collections (00-XX); Probability theory and stochastic processes (60-XX); Statistics (62-XX)

SWISS-MODEL

Software Authors:   T. Schwede, J. Kopp, N. Guex, M.C. Peitsch
Referenced in: 7 Publications (2006–2019)
Related Software: PROCHECK; MODELLER; BLAST; PSI-BLAST; I-TASSER; QMEAN; …
Main Fields: General and overarching topics; collections (00-XX); Computer science (68-XX); Biology and other natural sciences (92-XX)

ABySS

Software Authors:   Simpson, J.T., Wong, K., Jackman, S.D., Schein, J.E., Jones, S.J., Birol, I.
Referenced in: 12 Publications (2012–2021)
Related Software: Velvet; SPAdes; SOAPdenovo; IDBA-UD; GAGE; ALLPATHS; …
Main Fields: Combinatorics (05-XX); Statistics (62-XX); Computer science (68-XX)

iOri-Human

Software Authors:   Zhang, C.J.; Tang, H.; Li, W.C.
Referenced in: 13 Publications (2017–2022)
Related Software: iRNA-AI; pSuc-Lys; pLoc-mEuk; pLoc-mPlant; iPromoter-2L; iRSpot-EL; …
Main Fields: Statistics (62-XX); Computer science (68-XX); Biology and other natural sciences (92-XX)

MEME

Software Authors:   Bailey, T.L., Williams, N., Misleh, C., Li, W.W.
Referenced in: 9 Publications (2011–2018)
Related Software: BLAT; R; DIALIGN; ANNOVAR; KEGG; WEKA; …
Main Fields: General and overarching topics; collections (00-XX); Statistics (62-XX); Numerical analysis (65-XX)

AVID

Software Authors:   Bray, N., Dubchak, I., Pachter, L.
Referenced in: 9 Publications (2005–2022)
Related Software: BLAT; BLASTZ; MUMMER; LAGAN; ClustalW; DIALIGN; …
Main Fields: General and overarching topics; collections (00-XX); Probability theory and stochastic processes (60-XX); Statistics (62-XX)

Infernal

Software Authors:   Nawrocki EP, Kolbe DL, Eddy SR
Referenced in: 7 Publications (2010–2018)
Related Software: Rfam; R; ClustalW; Bioconductor; Mauve; Mugsy; …
Main Fields: General and overarching topics; collections (00-XX); Statistics (62-XX); Computer science (68-XX)

Bali-phy

Software Authors:   Suchard, M. A.; B. D. Redelings
Referenced in: 10 Publications (2009–2020)
Related Software: MrBayes; Statalign; MUSCLE; BEAST; ClustalW; CLUSTAL; …
Main Fields: Combinatorics (05-XX); Probability theory and stochastic processes (60-XX); Statistics (62-XX)

MAMMOTH

Software Authors:   Ortiz, A.R.; Strauss, C.E.M.; Olmea, O.
Referenced in: 8 Publications (2008–2017)
Related Software: TM-align; BLAST; PSI-BLAST; DIAL; GenThreader; PHYLIP; …
Main Fields: Statistics (62-XX); Numerical analysis (65-XX); Computer science (68-XX)

SVM-Prot

Software Authors:   –
Referenced in: 9 Publications (2006–2019)
Related Software: LIBSVM; Cell-PLoc; Cd-hit; GPCR-CA; Pfam; BLAST; …
Main Fields: Combinatorics (05-XX); Statistics (62-XX); Computer science (68-XX)

Jalview

Software Authors:   Clamp M, Cuff J, Searle SM et al
Referenced in: 1 Publication (2017)
Related Software: UniProt; MUSCLE; ClustalW; MrBayes; BMGE; CINEMA; …
Main Fields: General and overarching topics; collections (00-XX); Biology and other natural sciences (92-XX)

RSEARCH

Software Authors:   Klein, R. J.; Eddy, S. R.
Referenced in: 6 Publications (2004–2008)
Related Software: Rfam; Mfold; ClustalW; T-coffee; MARNA; STRAL; …
Main Fields: Probability theory and stochastic processes (60-XX); Numerical analysis (65-XX); Computer science (68-XX)

SSAHA

Software Authors:   Ning Z, Cox AJ, Mullikin JC
Referenced in: 3 Publications (2005–2016)
Related Software: Soap; BLAT; BLAST; PSI-BLAST; KEGG; SHRiMP; …
Main Fields: Statistics (62-XX); Computer science (68-XX); Biology and other natural sciences (92-XX)

BaCelLo

Software Authors:   Pierleoni A, Martelli PL, Fariselli P, Casadio R
Referenced in: 4 Publications (2012–2015)
Related Software: Cell-PLoc; MultiLoc; MultiLoc2; Plant-mPLoc; Euk-PLoc; Euk-mPLoc; …
Main Fields: General and overarching topics; collections (00-XX); Computer science (68-XX); Biology and other natural sciences (92-XX)

FUGUE

Software Authors:   Jiye Shi, Tom L Blundell, Kenji Mizuguchi
Referenced in: 4 Publications (2010–2016)
Related Software: GenThreader; MAFFT; PISCES; LIBSVM; Infernal; PROCHECK; …
Main Fields: General and overarching topics; collections (00-XX); Statistics (62-XX); Computer science (68-XX)

INDELible

Software Authors:   Fletcher W, Yang ZH
Referenced in: 7 Publications (2012–2021)
Related Software: SimPhy; ASTRID; DendroPy; RAxML; OCTAL; FastMe; …
Main Fields: General and overarching topics; collections (00-XX); Probability theory and stochastic processes (60-XX); Computer science (68-XX)

SABmark

Software Authors:   Walle, I.V., Lasters, I., Wyns, L.
Referenced in: 4 Publications (2013–2017)
Related Software: MUSCLE; ClustalW; OXBench; Kalign; ProbCons; Balibase; …
Main Fields: General and overarching topics; collections (00-XX); Statistics (62-XX); Biology and other natural sciences (92-XX)

SEGID

Software Authors:   Wang, L.; Xu, Y.
Referenced in: 8 Publications (2005–2011)
Related Software: MAVG; WebGestalt
Main Fields: Computer science (68-XX); Operations research, mathematical programming (90-XX)

JPred

Software Authors:   Cuff JA, Clamp ME, Siddiqui AS, Finlay M, Barton GJ
Referenced in: 2 Publications (2004)
Related Software: BLAST; PSI-BLAST; ProtVec; ACCpro; GitHub; SSpro; …
Main Fields: Operations research, mathematical programming (90-XX); Biology and other natural sciences (92-XX)

Rose

Software Authors:   J. Stoye, D. Evers, F. Meyer
Referenced in: 5 Publications (2008–2013)
Related Software: ClustalW; Clustal X; CLUSTAL; Pfam; Bali-phy; HMMoC; …
Main Fields: Statistics (62-XX); Numerical analysis (65-XX); Computer science (68-XX)

BS Seeker

Software Authors:   Chen, P. Y., S. J. Cokus, M. Pellegrini
Referenced in: 6 Publications (2012–2022)
Related Software: BSMAP; Bismark; BSmooth; Bowtie 2; SHRiMP; MethylCoder; …
Main Fields: General and overarching topics; collections (00-XX); Probability theory and stochastic processes (60-XX); Computer science (68-XX)

3DCoffee

Software Authors:   O. O’Sullivan, K. Suhre, C. Abergel, D. G. Higgins, C. Notredame
Referenced in: 5 Publications (2005–2016)
Related Software: ClustalW; ProbCons; T-coffee; MUSCLE; MAFFT; SABmark; …
Main Fields: History and biography (01-XX); Statistics (62-XX); Numerical analysis (65-XX)

DIALIGN-TX

Software Authors:   Subramanian AR, Kaufmann M, Morgenstern B
Referenced in: 4 Publications (2012–2017)
Related Software: DIALIGN; MUSCLE; T-coffee; ClustalW; Noisy; ProbCons; …
Main Fields: Computer science (68-XX); Operations research, mathematical programming (90-XX); Biology and other natural sciences (92-XX)

HHpred

Software Authors:   J. Söding, A. Biegert, A. Lupas
Referenced in: 3 Publications (2014–2018)
Related Software: Pfam; BioGRID; PSI-BLAST; ARACNE; KEGG; minet; …
Main Fields: General and overarching topics; collections (00-XX); Statistics (62-XX); Computer science (68-XX)

MEGA4

Software Authors:   Koichiro Tamura; Joel Dudley; Masatoshi Nei; Sudhir Kumar
Referenced in: 6 Publications (2009–2018)
Related Software: MEGA; MUSCLE; clusfind; MrBayes; PAL2NAL; DAMBE; …
Main Fields: Field theory and polynomials (12-XX); Statistics (62-XX); Numerical analysis (65-XX)

OXBench

Software Authors:   Raghava GPS, Searle SMJ, Audley PC, Barber JD, Barton GJ
Referenced in: 5 Publications (2008–2017)
Related Software: ClustalW; SABmark; MUSCLE; MrBayes; Mauve; Kalign; …
Main Fields: General and overarching topics; collections (00-XX); Statistics (62-XX); Biology and other natural sciences (92-XX)

Probalign

Software Authors:   Roshan U, Livesay DR
Referenced in: 4 Publications (2013–2017)
Related Software: MUSCLE; ClustalW; ProbCons; MAFFT; T-coffee; SABmark; …
Main Fields: Operations research, mathematical programming (90-XX); Biology and other natural sciences (92-XX)

RNAlign

Software Authors:   F Corpet, B Michot
Referenced in: 6 Publications (2000–2010)
Related Software: EzyPred; FoldRate; Euk-mPLoc; HIVcleave; Signal-CF; GPCR-CA; …
Main Fields: Combinatorics (05-XX); Statistics (62-XX); Numerical analysis (65-XX)

ScalaBLAST

Software Authors:   Oehmen, C.; Nieplocha, Jarek
Referenced in: 4 Publications (2008–2020)
Related Software: BLAST; k-means++; AS 136; PSI-BLAST; mpiBLAST; Silhouettes; …
Main Fields: Statistics (62-XX); Computer science (68-XX); Biology and other natural sciences (92-XX)

CloudBurst

Software Authors:   Michael C. Schatz
Referenced in: 2 Publications (2013–2018)
Related Software: Soap; MrsRF; MapReduce; BWA; ZOOM; Crossbow; …
Main Fields: Computer science (68-XX); Biology and other natural sciences (92-XX)

DIAL

Software Authors:   F. Ferrè; Y. Ponty; W. A. Lorenz; Peter Clote
Referenced in: 3 Publications (2008–2015)
Related Software: ARTS; MAMMOTH; FRASS; iPARTS; FR3D; SARSA; …
Main Fields: Computer science (68-XX); Biology and other natural sciences (92-XX)

GeneMarkS

Software Authors:   Besemer J, Lomsadze A, Borodovsky M
Referenced in: 4 Publications (2004–2017)
Related Software: UniProt; InterProScan; EasyGene; Prodigal; R; RegulonDB; …
Main Fields: General and overarching topics; collections (00-XX); Probability theory and stochastic processes (60-XX); Computer science (68-XX)

BEETL

Software Authors:   Cox, Anthony J.; Jakobi, Tobias; Rosone, Giovanna; Schulz-Trieglaff, Ole B.
Referenced in: 5 Publications (2012–2021)
Related Software: BWA; SlimGene; Kpath; SCALCE; ABySS; IDBA-UD; …
Main Fields: Computer science (68-XX); Biology and other natural sciences (92-XX)

ByteNet

Software Authors:   Nal Kalchbrenner, Lasse Espeholt, Karen Simonyan, Aaron van den Oord, Alex Graves, Koray Kavukcuoglu
Referenced in: 4 Publications (2017–2022)
Related Software: WaveNet; Adam; Tensor2Tensor; Xception; ImageNet; ConvS2S; …
Main Fields: Statistics (62-XX); Computer science (68-XX); Mechanics of deformable solids (74-XX)

GeneRAGE

Software Authors:   Anton J. Enright, Christos A. Ouzounis
Referenced in: 3 Publications (2004–2017)
Related Software: ProClust; MEME; SPADE; gmp; BWA; Bowtie 2; …
Main Fields: Statistics (62-XX); Computer science (68-XX); Biology and other natural sciences (92-XX)

MARNA

Software Authors:   Sven Siebert; Rolf Backofen
Referenced in: 3 Publications (2008–2015)
Related Software: Rfam; STRAL; ClustalW; MAFFT; T-coffee; RSEARCH; …
Main Fields: Computer science (68-XX); Biology and other natural sciences (92-XX)

Mugsy

Software Authors:   Samuel V. Angiuoli, Steven L. Salzberg
Referenced in: 4 Publications (2013–2022)
Related Software: MUSCLE; HMMER; Mauve; MrBayes; iGTP; ProtTest 3; …
Main Fields: General and overarching topics; collections (00-XX); Statistics (62-XX); Biology and other natural sciences (92-XX)

Noisy

Software Authors:   Dress AW, Flamm C, Fritzsch G, Grüunewald S, Kruspe M, Prohaska SJ, Stadler PF
Referenced in: 2 Publications (2017–2018)
Related Software: T-coffee; DIALIGN; DIALIGN-TX; SABmark; Clustal X; MUSCLE; …
Main Fields: Combinatorics (05-XX); Statistics (62-XX); Biology and other natural sciences (92-XX)

PairProSVM

Software Authors:   Mak, M.; Guo, J.; Kung, S.
Referenced in: 2 Publications (2011–2014)
Related Software: Cell-PLoc; MultiLoc; MultiLoc2; Euk-mPLoc; Gneg-mPLoc; Plant-mPLoc; …
Main Fields: Computer science (68-XX); Biology and other natural sciences (92-XX)

PROMALS

Software Authors:   Pei, Jimin; Kim, Bong-Hyun; Tang, Ming; Grishin, Nick V
Referenced in: 3 Publications (2011–2013)
Related Software: Kalign; MUSCLE; PCMA; T-coffee; MrBayes; Gegenees; …
Main Fields: Computer science (68-XX); Biology and other natural sciences (92-XX)

Scoredist

Software Authors:   Erik LL Sonnhammer; Volker Hollich
Referenced in: 3 Publications (2002–2022)
Related Software: FastTree; DEPP; PhyloGeoTool; INSTRAL; UShER; HmmUFOtu; …
Main Fields: Computer science (68-XX); Biology and other natural sciences (92-XX)

SLAM

Software Authors:   Alexandersson, M., Cawley, S., Pachter, L.
Referenced in: 3 Publications (2005–2015)
Related Software: BLAST; ECgene; PSI-BLAST; BLAT; ARACHNE; RePS; …
Main Fields: Probability theory and stochastic processes (60-XX); Operations research, mathematical programming (90-XX); Biology and other natural sciences (92-XX)

BFAST

Software Authors:   Homer, N., Merriman, B., Nelson, S.F.
Referenced in: 3 Publications (2010–2017)
Related Software: SHRiMP; PatternHunter; BWA; Soap; ART; GASSST; …
Main Fields: Computer science (68-XX); Biology and other natural sciences (92-XX)

Bio3d

Software Authors:   Barry Grant, Xin-Qiu Yao, Lars Skjaerven, Julien Ide
Referenced in: 2 Publications (2014–2021)
Related Software: RaptorX-Angle; GeoPCA; clusfind; conformalInference; k-means++; BAMBI; …
Main Fields: Statistics (62-XX); Biology and other natural sciences (92-XX)

BioGAP

Software Authors:   Attila Egry-Nagy; Andrew Francis; Volker Gebhardt
Referenced in: 4 Publications (2014–2019)
Related Software: Mauve; GAP; GitHub; VIZ; TikZ; Graphviz
Main Fields: Combinatorics (05-XX); Order, lattices, ordered algebraic structures (06-XX); Group theory and generalizations (20-XX)

C-GRAAL

Software Authors:   Vesna Memisevic; Natasa Przulj
Referenced in: 4 Publications (2013–2022)
Related Software: GEDEVO; SPINAL; CVX; SDPT3; Algorithm 97; ClustalW; …
Main Fields: Combinatorics (05-XX); Computer science (68-XX); Operations research, mathematical programming (90-XX)

CONTRAlign

Software Authors:   Do, Chuong B.; Gross, Samuel S.; Batzoglou, Serafim
Referenced in: 4 Publications (2006–2018)
Related Software: RNAforester; LIBLINEAR; MAFFT
Main Fields: Combinatorics (05-XX); Computer science (68-XX); Biology and other natural sciences (92-XX)

ECgene

Software Authors:   Kim, N., Shin, S., Lee, S.
Referenced in: 1 Publication (2015)
Related Software: SLAM; BLAT; ARACHNE; RePS; JBROWSE; ABySS; …
Main Fields: Probability theory and stochastic processes (60-XX); Operations research, mathematical programming (90-XX); Biology and other natural sciences (92-XX)

iPARTS

Software Authors:   C. W. Wang, K. T. Chen, C. L. Lu
Referenced in: 3 Publications (2014–2015)
Related Software: DIAL; MAMMOTH; FRASS; Bio3d; MCQ4Structures; Jmol; …
Main Fields: General and overarching topics; collections (00-XX); Computer science (68-XX); Biology and other natural sciences (92-XX)

jpHMM

Software Authors:   A.-K. Schultz, I. Bulla, M. Abdou-Chekaraou, E. Gordien, B. Morgenstern, F. Zoulim, P. Dény, M. Stanke
Referenced in: 1 Publication (2011)
Related Software: CONSEL; Scoredist; HyPhy; RDP2; SplitsTree; Seq-Gen
Main Fields: Statistics (62-XX); Biology and other natural sciences (92-XX)

M-Coffee

Software Authors:   Wallace IM, O’Sullivan O, Higgins DG et al
Referenced in: 3 Publications (2014–2017)
Related Software: Kalign; MUSCLE; MAFFT; OXBench; UniProt; SABmark; …
Main Fields: General and overarching topics; collections (00-XX); Probability theory and stochastic processes (60-XX); Biology and other natural sciences (92-XX)

MUMMALS

Software Authors:   Pei J, Grishin NV
Referenced in: 3 Publications (2015–2017)
Related Software: MUSCLE; ClustalW; ProbCons; MAFFT; T-coffee; Balibase; …
Main Fields: Statistics (62-XX); Operations research, mathematical programming (90-XX); Biology and other natural sciences (92-XX)

PartTree

Software Authors:   Katoh, K., Toh, H.
Referenced in: 3 Publications (2008–2016)
Related Software: ClustalW; OXBench; SABmark; Kalign; MUSCLE; ProbCons; …
Main Fields: Statistics (62-XX); Biology and other natural sciences (92-XX)

PCMA

Software Authors:   Pei J, Sadreyev R, Grishin NV
Referenced in: 4 Publications (2011–2017)
Related Software: T-coffee; MUSCLE; Kalign; Probalign; MUMMALS; DIALIGN-TX; …
Main Fields: Computer science (68-XX); Operations research, mathematical programming (90-XX); Biology and other natural sciences (92-XX)

PHYLO_WIN

Software Authors:   Galtier N, Gouy M, Gautier C
Referenced in: 2 Publications (2010–2017)
Related Software: SEAVIEW; CINEMA; Jalview; UniProt; Hetero; SplitsTree; …
Main Fields: General and overarching topics; collections (00-XX); Probability theory and stochastic processes (60-XX); Statistics (62-XX)

rVISTA

Software Authors:   Gabriela G. Loots, Ivan Ovcharenko
Referenced in: 2 Publications (2011–2016)
Related Software: KEGG; T-coffee; ClustalW; UniPROBE; InteroPORC; JASPAR; …
Main Fields: General and overarching topics; collections (00-XX); Computer science (68-XX); Biology and other natural sciences (92-XX)

SARSA

Software Authors:   Yen-Fu Chang; Yen-Lin Huang; Chin Lung Lu
Referenced in: 2 Publications (2009–2015)
Related Software: FR3D; DIAL; ARTS; SCOPmap; TM-align; BioJava; …
Main Fields: Computer science (68-XX); Biology and other natural sciences (92-XX)

SEAVIEW

Software Authors:   Galtier N, Gouy M, Gautier C
Referenced in: 2 Publications (2010–2017)
Related Software: PHYLO_WIN; CINEMA; Jalview; UniProt; Hetero; SplitsTree; …
Main Fields: General and overarching topics; collections (00-XX); Probability theory and stochastic processes (60-XX); Statistics (62-XX)

SNVMix

Software Authors:   Goya, R. et al.
Referenced in: 3 Publications (2012–2018)
Related Software: VarScan; RSEM; STAR; edgeR; Sniper; GlfMultiples; …
Main Fields: General and overarching topics; collections (00-XX); Biology and other natural sciences (92-XX)

SOAP3

Software Authors:   C.-M. Liu, T. Wong, E. Wu et al.
Referenced in: 4 Publications (2013–2018)
Related Software: BWA; Bowtie 2; Soap; deBGA; EMBOSS; libgapmis; …
Main Fields: Computer science (68-XX); Biology and other natural sciences (92-XX)

AL2CO

Software Authors:   Pei, J.; Grishin, N.
Referenced in: 2 Publications (2010–2011)
Related Software: MPRAP; AAindex; ClustalW; TMBpro; R; H2r; …
Main Fields: Statistics (62-XX); Biology and other natural sciences (92-XX)

ASPIC

Software Authors:   Bonizzoni P, Rizzi R, Pesole G
Referenced in: 1 Publication (2015)
Related Software: ASTALAVISTA; Exogean; EMIRGE; ViennaRNA; TagCleaner; OligoWalk; …
Main Fields: General and overarching topics; collections (00-XX); Biology and other natural sciences (92-XX)

BMGE

Software Authors:   Criscuolo A, Gribaldo S
Referenced in: 2 Publications (2014–2017)
Related Software: MrBayes; MUSCLE; Jalview; M-Coffee; AWTY; Cd-hit; …
Main Fields: General and overarching topics; collections (00-XX); Probability theory and stochastic processes (60-XX); Biology and other natural sciences (92-XX)

CINEMA

Software Authors:   Parry-Smith, D.J., Payne, A.W.R, Michie, A.D., Attwood, T.K.
Referenced in: 1 Publication (2017)
Related Software: PHYLO_WIN; SEAVIEW; Jalview; UniProt; MUSCLE; Hetero; …
Main Fields: General and overarching topics; collections (00-XX); Biology and other natural sciences (92-XX)

FastLSA

Software Authors:   Driga, Adrian; Lu, Paul; Schaeffer, Jonathan; Szafron, Duane; Charter, Kevin; Parsons, Ian
Referenced in: 2 Publications (2006–2008)
Related Software: ABySS; ClustalW; EMBOSS; mpiBLAST; CUDA
Main Fields: Computer science (68-XX); Biology and other natural sciences (92-XX)

GEDEVO

Software Authors:   Ibragimov, Rashid; Malek, Maximilian; Guo, Jiong; Baumbach, Jan
Referenced in: 2 Publications (2013–2022)
Related Software: C-GRAAL; GREAT; BioGRID; IGLOO; CVX; SDPT3; …
Main Fields: Combinatorics (05-XX); Operations research, mathematical programming (90-XX); Biology and other natural sciences (92-XX)

GMAP

Software Authors:   Wu TD, Watanabe CK
Referenced in: 2 Publications (2015–2016)
Related Software: BLAT; TopHat; C4.5; PHRAP; CAP3; Galaxy; …
Main Fields: Probability theory and stochastic processes (60-XX); Statistics (62-XX); Operations research, mathematical programming (90-XX)

GridBlast

Software Authors:   –
Referenced in: 2 Publications (2004–2010)
Related Software: mpiBLAST; Globus Toolkit; BLAST; PackageBLAST; Gbtk; BLAST++; …
Main Fields: Computer science (68-XX); Biology and other natural sciences (92-XX)

HHblits

Software Authors:   Remmert M, Biegert A, Hauser A, Söding J
Referenced in: 3 Publications (2016–2022)
Related Software: MUSCLE; UniProt; T-coffee; ClustalW; DIALIGN; SPAdes; …
Main Fields: General and overarching topics; collections (00-XX); Statistics (62-XX); Computer science (68-XX)

HubAlign

Software Authors:   Somaye Hashemifar; Jinbo Xu
Referenced in: 3 Publications (2015–2020)
Related Software: IsoRank; NETAL; GHOST; SPINAL; DeepWalk; node2vec; …
Main Fields: Combinatorics (05-XX); Computer science (68-XX); Operations research, mathematical programming (90-XX)

IPknot

Software Authors:   Sato K, Kato Y, Hamada M, Akutsu T, Asai K
Referenced in: 3 Publications (2012–2017)
Related Software: jViz.Rna; Mfold; GitHub; EMIRGE; ViennaRNA; TagCleaner; …
Main Fields: General and overarching topics; collections (00-XX); Combinatorics (05-XX); Computer science (68-XX)

L-GRAAL

Software Authors:   Noël Malod-Dognin; Nataša Pržulj
Referenced in: 3 Publications (2015–2021)
Related Software: IsoRank; GHOST; MAGNA++; SPINAL; PrimAlign; IsoRankN; …
Main Fields: Combinatorics (05-XX); Computer science (68-XX); Operations research, mathematical programming (90-XX)

MI-GRAAL

Software Authors:   Oleksii Kuchaiev; Natasa Przulj
Referenced in: 2 Publications (2013–2020)
Related Software: IsoRankN; IsoRank; Natalie; GHOST; NABEECO; SPINAL; …
Main Fields: Combinatorics (05-XX); Statistics (62-XX); Computer science (68-XX)

MSAProbs

Software Authors:   Y. Liu, B. Schmidt, and D. L. Maskell
Referenced in: 2 Publications (2013–2017)
Related Software: T-coffee; Probalign; Kalign; MUSCLE; ClustalW; ProbCons; …
Main Fields: Biology and other natural sciences (92-XX)

MTRAP

Software Authors:   Hara, Toshihide; Sato, Keiko; Ohya, Masanori
Referenced in: 2 Publications (2010–2013)
Related Software: Probalign; SABmark; Clustal X; T-coffee; MUSCLE; ClustalW; …
Main Fields: Dynamical systems and ergodic theory (37-XX); Biology and other natural sciences (92-XX)

MuSiC

Software Authors:   Yin Te Tsai, Yen Pin Huang, Ching Ta Yu, Chin Lung Lu
Referenced in: 3 Publications (2007)
Related Software: PROSITE; PSIPRED
Main Fields: Numerical analysis (65-XX); Computer science (68-XX); Operations research, mathematical programming (90-XX)

NAST

Software Authors:   T. Z. DeSantis, Jr., P. Hugenholtz, K. Keller, E. L. Brodie, N. Larsen, Y. M. Piceno, R. Phan, G. L. Andersen
Referenced in: 2 Publications (2013–2015)
Related Software: MrBayes; Gegenees; POY; MLTreeMap; SEPP; GapCoder; …
Main Fields: Computer science (68-XX); Biology and other natural sciences (92-XX)

PAL2NAL

Software Authors:   Suyama, M.; Torrents, D.; Bork, P.
Referenced in: 1 Publication (2018)
Related Software: MrBayes; PAML; DAMBE; MUSCLE; MEGA; MODELTEST; …
Main Fields: Biology and other natural sciences (92-XX)