• SALBPGen

  • Referenced in 20 articles [sw14513]
  • SALBPGen - A systematic data generator for (simple) assembly line balancing. Assembly line balancing ... extensively researched decision problem which arises when assembly line production systems are designed and operated ... instance generator for the simple assembly line balancing problem (SALBP) which can be applied ... other assembly line balancing problem, too. It is able to systematically create instances with very...
  • Slatec

  • Referenced in 34 articles [sw04367]
  • Energy Laboratories. The objective is to cooperatively assemble and install at each site a mathematical...
  • Chimera

  • Referenced in 34 articles [sw10908]
  • related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles...
  • BLAT

  • Referenced in 34 articles [sw16891]
  • only be computed once for each genome assembly. BLAT has several major stages. It uses...
  • p1afem

  • Referenced in 32 articles [sw08489]
  • method (AFEM). This includes functions for the assembly of the data, different error estimators...
  • MEGA

  • Referenced in 32 articles [sw09078]
  • MEGA provides many convenient facilities for the assembly of sequence data sets from files...
  • ALLPATHS

  • Referenced in 15 articles [sw06112]
  • ALLPATHS-LG is a whole-genome shotgun assembler that can generate high-quality genome assemblies ... significant difference between ALLPATHS and traditional assemblers such as Arachne is that ALLPATHS assemblies ... that has been absent from previous genome assemblies...
  • CAP3

  • Referenced in 16 articles [sw08935]
  • CAP3: A DNA Sequence Assembly Program. We describe the third generation of the CAP sequence ... assembly program. The CAP3 program includes a number of improvements and new features. The program ... also uses forward–reverse constraints to correct assembly errors and link contigs. Results of CAP3...
  • I-TASSER

  • Referenced in 18 articles [sw17207]
  • structure and function prediction. The iterative threading assembly refinement (I-TASSER) server is an integrated ... from multiple threading alignments and iterative structural assembly simulations. The function of the protein...
  • SPAdes

  • Referenced in 12 articles [sw17004]
  • SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing. The lion ... gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell ... chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell ... assembly, and demonstrate that it improves on the recently released E+V−SC assembler (specialized...
  • ABySS

  • Referenced in 12 articles [sw17343]
  • ABySS: a parallel assembler for short read sequence data. Widespread adoption of massively parallel deoxyribonucleic ... recent development of de novo short read assembly algorithms. A common shortcoming of the available ... tools is their inability to efficiently assemble vast amounts of data generated from large-scale ... address this limitation, we developed ABySS (Assembly By Short Sequences), a parallelized sequence assembler...
  • MEGAN

  • Referenced in 17 articles [sw33189]
  • environmental fosmid and BAC clones, or environmental assemblies. Emerging sequencing-by-synthesis technologies with very ... dissected without the need for assembly or the targeting of specific phylogenetic markers. It provides...
  • SUGGAR

  • Referenced in 14 articles [sw08883]
  • general capability moving body overset grid assembly. The Structured, Unstructured, and Generalized overset Grid AssembleR ... SUGGAR) code is an overset grid assembly program designed for moving body simulations that...
  • 2-ANTBAL

  • Referenced in 11 articles [sw19724]
  • colony optimisation algorithm for balancing two-sided assembly lines. Two-sided assembly lines ... special type of assembly lines in which workers perform assembly tasks in both sides ... crucial importance, especially in the assembly of large-sized products, like automobiles, buses or trucks ... address the two-sided mixed-model assembly line balancing problem. First, a mathematical programming model...
  • GAGE

  • Referenced in 11 articles [sw13528]
  • GAGE: a critical evaluation of genome assemblies and assembly algorithms. GAGE is an evaluation ... very latest large-scale genome assembly algorithms. We have organized this ”bake ... produce a realistic assessment of genome assembly software in a rapidly changing field of next ... Research: GAGE: A critical evaluation of genome assemblies and assembly algorithms...
  • IBM PC Assembler

  • Referenced in 12 articles [sw34510]
  • assembler language and programming; INTEL 8080, 8086, 80286, 80386, 80486, 80x86 assembly language...
  • ARACHNE

  • Referenced in 9 articles [sw07552]
  • ARACHNE: a whole-genome shotgun assembler. We describe a new computer system, called ARACHNE ... assembling genome sequence using paired-end whole-genome shotgun reads. ARACHNE has several key features ... achieves high accuracy by correcting errors before assembly, read merger based on forward-reverse links ... human chromosomes 21 and 22. The assemblies of these simulated reads yielded nearly complete coverage...
  • SHARCGS

  • Referenced in 9 articles [sw29573]
  • fast and highly accurate short-read assembly algorithm for de novo genomic sequencing. The latest ... sequencing, we developed the SHARCGS algorithm to assemble short-read (25–40-mer) data with ... show that 30-mer-based BAC assemblies have N50 sizes >20 kbp for Drosophila ... wrong base calls into account. We assembled 949,974 contigs with length...
  • ANTBAL

  • Referenced in 11 articles [sw02549]
  • colony optimization algorithm for balancing mixed-model assembly lines. The proposed algorithm accounts for zoning ... minimize the number of operators in the assembly line for a given cycle time ... account for in balancing mixed-model assembly lines. Computational experience shows the superior performance...
  • RSEM

  • Referenced in 11 articles [sw17160]
  • important for quantification with de novo transcriptome assemblies in the absence of sequenced genomes ... combination with a de novo transcriptome assembler, RSEM enables accurate transcript quantification for species without ... useful for quantification with de novo transcriptome assemblies. In addition, RSEM has enabled valuable guidance...