• PMA

  • Referenced in 120 articles [sw19126]
  • correlation analysis, with applications to genomic data. Statistical Applications in Genetics and Molecular Biology...
  • PAUP*

  • Referenced in 57 articles [sw07834]
  • high-speed computer analysis of molecular, morphological and/or behavioral data to infer phylogenetic relationships ... biology, ecology, and forensic studies. The success of previous versions of PAUP: Phylogenetic Analysis Using ... combinability of data and permutation tests for nonrandomness of data structure. These, along with many ... even more indispensable tool in comparative biological analysis than were previous editions of the program...
  • clustervalidation

  • Referenced in 32 articles [sw34195]
  • application to post-genomic data analysis. Synthetic and real biological datasets are used to demonstrate...
  • SHOGUN

  • Referenced in 103 articles [sw03517]
  • Markov models, multiple kernel learning, linear discriminant analysis, and more. Most of the specific algorithms ... different data classes. We have used this toolbox in several applications from computational biology, some...
  • CGAL

  • Referenced in 380 articles [sw00118]
  • design and modeling, geographic information systems, molecular biology, medical imaging, robotics and motion planning, mesh ... Computational Geometry Algorithms Library (CGAL), offers data structures and algorithms like triangulations (2D constrained triangulations ... neighbor interpolation and placement of streamlines), shape analysis, fitting, and distances (smallest enclosing sphere...
  • REVEAL

  • Referenced in 28 articles [sw36999]
  • maximize functional inference from such large data sets. Is it possible, in principle, to completely ... inputs per element), the analysis of incomplete state transition tables (100 state transition pairs ... essentially allowing direct application to realistic biological data sets. The ability to adequately solve ... inverse problem may enable in-depth analysis of complex dynamic systems in biology and other...
  • VMD

  • Referenced in 86 articles [sw18651]
  • designed for modeling, visualization, and analysis of biological systems such as proteins, nucleic acids, lipid ... molecules, as VMD can read standard Protein Data Bank (PDB) files and display the contained...
  • EMBOSS

  • Referenced in 35 articles [sw10917]
  • Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet ... user community. The software automatically copes with data in a variety of formats and even ... allows transparent retrieval of sequence data from the web. Also, as extensive libraries are provided ... currently available packages and tools for sequence analysis into a seamless whole. EMBOSS breaks...
  • DAISY

  • Referenced in 46 articles [sw09059]
  • parameters can be uniquely recovered from observed data is essential before investing resources, time ... biomedical experiments. Many interesting biological models are nonlinear but identifiability analysis for nonlinear system turns...
  • PAGE

  • Referenced in 7 articles [sw23828]
  • enrichment analysis (GSEA) is a microarray data analysis method that uses predefined gene sets ... genes to identify significant biological changes in microarray data sets. GSEA is especially useful when ... level analysis methods or different microarray platforms. Comparison of two aged muscle microarray data sets ... identify significantly changed biological themes from microarray data irrespective of analysis methods or microarray platforms...
  • PyDSTool

  • Referenced in 17 articles [sw06718]
  • bifurcation analysis, data analysis, and other tools for modeling -- particularly for biological applications. The project...
  • Mesquite

  • Referenced in 15 articles [sw09680]
  • system for evolutionary analysis. Mesquite is modular, extendible software for evolutionary biology, designed to help ... biologists organize and analyze comparative data about organisms. Its emphasis is on phylogenetic analysis...
  • explorase

  • Referenced in 2 articles [sw25156]
  • Systems Biology. GUI for exploratory data analysis of systems biology data...
  • SeqinR

  • Referenced in 4 articles [sw08300]
  • Analysis. Exploratory data analysis and data visualization for biological sequence (DNA and protein) data. Include...
  • DAMBE

  • Referenced in 2 articles [sw17192]
  • DAMBE: Software package for data analysis in molecular biology and evolution. DAMBE (data analysis ... graphically describing, and analyzing molecular sequence data with a user-friendly Windows 95/98/2000/NT interface. DAMBE...
  • GOSim

  • Referenced in 5 articles [sw08204]
  • producing large amounts of biological data. During the analysis of such data often there ... used to cluster genes according to their biological function. Vice versa, they can also ... data. Since version 1.1 GOSim additionally offers the possibility of a GO enrichment analysis using...
  • BicPAMS

  • Referenced in 2 articles [sw29990]
  • BicPAMS: software for biological data analysis with pattern-based biclustering. BicPAMS is a powerful ... exploratory and unsupervised analysis of tabular and network data. BicPAMS integrates state ... tested on biomedical data (including expression data, clinical data and biological networks) and social data...
  • edgeR

  • Referenced in 52 articles [sw06936]
  • genomics applications. One of the fundamental data analysis tasks, especially for gene expression studies, involves ... count data. An overdispersed Poisson model is used to account for both biological and technical...
  • SeqAn

  • Referenced in 6 articles [sw19473]
  • structures for the analysis of sequences with the focus on biological data. Our library applies...
  • jHoles

  • Referenced in 7 articles [sw15020]
  • topological data analysis are one of the promising tools in the study of biological systems...