• SHEEP

  • Referenced in 37 articles [sw00855]
  • This version was written in the assembly language MACRO-10 for DEC-10 computers...
  • p1afem

  • Referenced in 36 articles [sw08489]
  • method (AFEM). This includes functions for the assembly of the data, different error estimators...
  • BLAT

  • Referenced in 36 articles [sw16891]
  • only be computed once for each genome assembly. BLAT has several major stages. It uses...
  • Slatec

  • Referenced in 35 articles [sw04367]
  • Energy Laboratories. The objective is to cooperatively assemble and install at each site a mathematical...
  • MEGA

  • Referenced in 34 articles [sw09078]
  • MEGA provides many convenient facilities for the assembly of sequence data sets from files...
  • Chimera

  • Referenced in 34 articles [sw10908]
  • related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles...
  • 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 17 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...
  • SUGGAR

  • Referenced in 15 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...
  • 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...
  • TSFC

  • Referenced in 23 articles [sw20272]
  • code that carries out the finite element assembly. In this paper we present...
  • 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...
  • 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...