• XPath

  • Referenced in 370 articles [sw15780]
  • XPath 2.0 Data Model (Second Edition)]. The data model provides a tree representation ... such as integers, strings, and booleans, and sequences that may contain both references to nodes ... value, or more generally, any sequence allowed by the data model. The name...
  • edgeR

  • Referenced in 46 articles [sw06936]
  • examining differential expression of replicated count data. An overdispersed Poisson model is used to account ... software may have other applications beyond sequencing data, such as proteome peptide count data...
  • CUBLAS

  • Referenced in 75 articles [sw06880]
  • memory space, fill them with data, call the sequence of desired CUBLAS functions, and then ... provides helper functions for writing and retrieving data from...
  • EMBOSS

  • Referenced in 34 articles [sw10917]
  • even allows transparent retrieval of sequence data from the web. Also, as extensive libraries ... currently available packages and tools for sequence analysis into a seamless whole. EMBOSS breaks...
  • MEGA

  • Referenced in 32 articles [sw09078]
  • designed for comparative analysis of homologous gene sequences either from multigene families or from different ... tools for statistical analysis of data, MEGA provides many ... convenient facilities for the assembly of sequence data sets from files or web-based repositories...
  • DIALIGN

  • Referenced in 33 articles [sw12015]
  • therefore be applied to sequence data that cannot be correctly aligned by more traditional approaches...
  • iRSpot-TNCPseAAC

  • Referenced in 31 articles [sw22412]
  • ever-increasing amount of genome sequence data in the postgenomic era, computational methods for effectively ... incorporate its local or short-rage sequence order information; while the latter, its global...
  • BIONJ

  • Referenced in 29 articles [sw08301]
  • based on a simple model of sequence data. We propose an improved version ... when these estimates are obtained from aligned sequences. At each step it permits the selection...
  • Samtools

  • Referenced in 20 articles [sw14583]
  • programs for interacting with high-throughput sequencing data. It consists of three separate repositories: Samtools ... calling/filtering summarising SNP and short indel sequence variants. HTSlib ... library for reading/writing high-throughput sequencing data. Samtools and BCFtools both use HTSlib internally...
  • iSNO-AAPair

  • Referenced in 24 articles [sw22447]
  • biological experiments. Facing the explosive protein sequence data generated in the post-genomic...
  • ape

  • Referenced in 55 articles [sw04569]
  • from allelic and nucleotide data, reading and writing nucleotide sequences, and several tools such ... generalized skyline plots, graphical exploration of phylogenetic data (alex, trex, kronoviz), estimation of absolute evolutionary...
  • PISCES

  • Referenced in 31 articles [sw16873]
  • culling sets of protein sequences from the Protein Data Bank (PDB) by sequence identity...
  • GATK

  • Referenced in 14 articles [sw12019]
  • framework for analyzing next-generation DNA sequencing data. Next-generation DNA sequencing (NGS) projects, such ... genetic variation among individuals. However, the massive data sets generated by NGS—the 1000 Genome ... complexity of accessing and manipulating the data produced by these machines. Here, we discuss ... robust analysis tools for next-generation DNA sequencers using the functional programming philosophy of MapReduce...
  • DEseq

  • Referenced in 48 articles [sw10344]
  • variance-mean dependence in count data from high-throughput sequencing assays and test for differential...
  • ABySS

  • Referenced in 12 articles [sw17343]
  • parallel assembler for short read sequence data. Widespread adoption of massively parallel deoxyribonucleic acid ... sequencing instruments has prompted the recent development of de novo short read assembly algorithms ... assemble vast amounts of data generated from large-scale sequencing projects, such as the sequencing...
  • SPADE

  • Referenced in 87 articles [sw02226]
  • techniques, and using simple join operations. All sequences are discovered in only three database scans ... data. It also has linear scalability with respect to the number of input-sequences...
  • BioJava

  • Referenced in 13 articles [sw05334]
  • also read and write sequence data in a variety of common formats and communicate with...
  • Notung

  • Referenced in 12 articles [sw08917]
  • hand. The rapid growth of genetic sequence data will soon allow similar studies...
  • MUSCLE

  • Referenced in 71 articles [sw13193]
  • large numbers of sequences, aligning 5000 sequences of average length ... MUSCLE program, source code and PREFAB test data are freely available at http://www.drive5. com/muscle...
  • iOri-Human

  • Referenced in 12 articles [sw23955]
  • results in a huge amount of sequence data, it is highly desired to develop computational ... existing computational methods, such as sequence alignment or kmer strategies, it could hardly achieve decent...