• PSI-BLAST

  • Referenced in 226 articles [sw17324]
  • with a new heuristic for generating gapped alignments, yields a gapped BLAST program that runs ... introduced for automatically combining statistically significant alignments produced by BLAST into a position-specific score...
  • BLAST

  • Referenced in 241 articles [sw17334]
  • Basic Local Alignment Search Tool. BLAST finds regions of similarity between biological sequences. The program...
  • ClustalW

  • Referenced in 133 articles [sw12016]
  • improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties...
  • MUSCLE

  • Referenced in 71 articles [sw13193]
  • Muscle: multiple sequence alignment with high accuracy and high throughput. We describe MUSCLE ... computer program for creating multiple alignments of protein sequences. Elements of the algorithm include fast ... distance estimation using kmer counting, progressive alignment using a new profile function we call ... CLUSTALW on four test sets of reference alignments: BAliBASE, SABmark, SMART and a new benchmark...
  • T-coffee

  • Referenced in 39 articles [sw13195]
  • method for fast and accurate multiple sequence alignment. We describe a new method (T-Coffee ... multiple sequence alignment that provides a dramatic improvement in accuracy with a modest sacrifice ... popular progressive approach to multiple alignment but avoids the most serious pitfalls caused ... data set of all pair-wise alignments between the sequences. This provides us with...
  • MAFFT

  • Referenced in 41 articles [sw08304]
  • MAFFT: Multiple alignment program for amino acid or nucleotide sequences. MAFFT is a multiple sequence ... alignment program for unix-like operating systems. It offers a range of multiple alignment methods ... accurate; for alignment of <∼200 sequences), FFT-NS-2 (fast; for alignment...
  • MUMMER

  • Referenced in 39 articles [sw17256]
  • MUMmer Ultra-fast alignment of large-scale DNA and protein sequences. MUMmer is a system ... rapidly aligning entire genomes, whether in complete or draft form. For example, MUMmer ... Linux desktop computer. MUMmer can also align incomplete genomes; it can easily handle the 100s ... from a shotgun sequencing project, and will align them to another set of contigs...
  • LFW

  • Referenced in 43 articles [sw31362]
  • original and three different types of ”aligned” images. The aligned images include ”funneled images” (ICCV ... which uses an unpublished method of alignment, and ”deep funneled” images (NIPS 2012). Among these...
  • BLAT

  • Referenced in 34 articles [sw16891]
  • BLAT — The BLAST-Like Alignment Tool. Analyzing vertebrate genomes requires rapid mRNA/DNA and cross-species ... protein alignments. A new tool, BLAT, is more accurate and 500 times faster than popular ... existing tools for mRNA/DNA alignments and 50 times faster for protein alignments at sensitivity settings ... query sequence. It performs an alignment between homologous regions. It stitches together these aligned regions...
  • BWA

  • Referenced in 45 articles [sw34374]
  • Burrows-Wheeler Aligner: BWA is a software package for mapping low-divergent sequences against ... such as long-read support and split alignment, but BWA-MEM, which is the latest...
  • DIALIGN

  • Referenced in 33 articles [sw12015]
  • DIALIGN: multiple DNA and protein sequence alignment at BiBiServ. DIALIGN is a widely used software ... tool for multiple DNA and protein sequence alignment. The program combines local and global alignment ... sequence data that cannot be correctly aligned by more traditional approaches. DIALIGN is available online ... features. To compare the output of different alignment programs, we developed the program AltAVisT...
  • Soap

  • Referenced in 37 articles [sw08915]
  • SOAP: short oligonucleotide alignment program. We have developed a program SOAP for efficient gapped ... ungapped alignment of short oligonucleotides onto reference sequences. The program is designed to handle...
  • knitr

  • Referenced in 49 articles [sw11224]
  • width and height as well as alignment of plots in the output document...
  • MODELLER

  • Referenced in 33 articles [sw27731]
  • structures (1,2). The user provides an alignment of a sequence to be modeled with ... flexibly defined objective function, multiple alignment of protein sequences and/or structures, clustering, searching of sequence...
  • PISCES

  • Referenced in 31 articles [sw16873]
  • sequence identities are obtained from PSI-BLAST alignments with position-specific substitution matrices derived from ... identity and often overestimates sequence identity by aligning only well-conserved fragments. PDB sequences...
  • FAIR.m

  • Referenced in 42 articles [sw34733]
  • integrated. Is is also known as alignment, co-registration, fusion, optical flow, or warping...
  • TopHat

  • Referenced in 22 articles [sw17157]
  • TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. TopHat ... popular spliced aligner for RNA-sequence (RNA-seq) experiments. In this paper, we describe TopHat2 ... many significant enhancements to TopHat. TopHat2 can align reads of various lengths produced ... genome. In addition to de novo spliced alignment, TopHat2 can align reads across fusion breaks...
  • Balibase

  • Referenced in 28 articles [sw08913]
  • BAliBASE: a benchmark alignment database for the evaluation of multiple alignment programs...
  • Clustal X

  • Referenced in 28 articles [sw16249]
  • Clustal W and Clustal X multiple sequence alignment programs have been completely rewritten ... will facilitate the further development of the alignment algorithms in the future and has allowed...
  • PhyloNetwork

  • Referenced in 27 articles [sw28216]
  • PhyloNetwork: A perl package and an alignment tool for phylogenetic networks. Phylogenetic networks ... networks by computing distances between them or aligning them. Results: In order to improve this...