Search results

• MMseqs2
  ...ing) is a software suite to search and cluster huge protein and nucleotide sequence sets. MMseqs2 is open source GPL-licensed software implemented in C++ for L ...Soeding J. MMseqs2 desktop and local web server app for fast, interactive sequence searches. Bioinformatics, doi: 10.1093/bioinformatics/bty1057 (2019).]
  3 KB (413 words) - 20:22, 2 October 2023
• Wise
  ...e focused on comparisons of biopolymers, commonly DNA sequence and protein sequence. There are many other packages which do this, probably the best known being
  3 KB (321 words) - 21:29, 6 December 2019
• SNP-Pipeline
  SNP Pipeline is a pipeline for the production of SNP matrices from sequence data used in the phylogenetic analysis of pathogenic organisms sequenced fr ...ne: an automated method for constructing SNP matrices from next-generation sequence data. PeerJ Computer Science 1:e20 https://doi.org/10.7717/peerj-cs.20]
  3 KB (306 words) - 17:00, 10 June 2022
• Catch
  ...ackage for designing probe sets to use for nucleic acid capture of diverse sequence. of species. It allows blacklisting sequence from the design (e.g., background in microbial enrichment),
  3 KB (422 words) - 18:23, 12 August 2022
• DeconSeq
  The DeconSeq tool can be used to automatically detect and efficiently remove sequence contaminations from genomic and metagenomic datasets. It is easily configur ...med/21278185 Schmieder R and Edwards R: Fast identification and removal of sequence contamination from genomic and metagenomic datasets. PLoS ONE 2011, 6:e1728
  3 KB (299 words) - 17:00, 10 June 2022
• Recycler
  ...from sequence data of isolate microbial genomes, plasmidome and metagenome sequence data.
  3 KB (297 words) - 14:21, 11 October 2022
• FSA
  ...using only pairwise estimations of homology. This is made possible by the sequence annealing technique for constructing a multiple alignment from pairwise com
  3 KB (307 words) - 20:38, 23 May 2022
• Ancestryhmm
  ...neously estimating local ancestry and admixture time using next generation sequence data in samples of arbitrary ploidy. ...neously estimating local ancestry and admixture time using next generation sequence data in samples of arbitrary ploidy. PLoS genetics, 13(1), p.e1006529.
  2 KB (291 words) - 21:25, 9 May 2023
• AliStat
  Multiple sequence alignments may contain a variety of completely-specified characters. Here a for multiple sequence alignments. NAR Genomics and Bioinformatics 2 (2), lqaa024.
  3 KB (315 words) - 20:18, 1 October 2020
• REPdenovo
  REPdenovo is designed for constructing repeats directly from sequence reads. It based on the idea of frequent k-mer assembly. REPdenovo provides ...elsen and Yufeng Wu, REPdenovo: Inferring de novo repeat motifs from short sequence reads, PLoS One 11.3 (2016): e0150719.]
  3 KB (327 words) - 21:43, 21 August 2022
• SeSiMCMC
  The Sequence Similarities by Markov Chain Monte Carlo (SeSiMCMC) algorithm careful Bayesian analysis to consider site absence in a sequence.
  3 KB (299 words) - 22:41, 21 August 2022
• HLAminer
  ...and align the resulting contigs to reference HLA alleles from the IMGT/HLA sequence repository using commodity hardware with standard specifications (<2GB RAM, ...novo assembly of all recruited reads, a set of contigs is generated. Only sequence contigs equal or larger than 200nt in length are considered for further ana
  4 KB (541 words) - 14:55, 14 December 2022
• Magus
  MAGUS is a tool for piecewise large-scale multiple sequence alignment. Original MAGUS paper: Smirnov, V. and Warnow, T., 2020. MAGUS: Multiple Sequence Alignment using Graph Clustering. Bioinformatics. https://doi.org/10.1093/b
  3 KB (327 words) - 17:51, 16 March 2022
• CRISP
  ...d using the Illumina sequencing platform. In principle, it should work for sequence data from other sequencing platforms. The method requires each pool to be s
  3 KB (342 words) - 21:01, 6 December 2019
• MetaCluster
  ...nomic sequences. Existing binning methods based on sequence similarity and sequence composition markers rely heavily on the reference genomes of known microorg
  3 KB (321 words) - 19:26, 18 August 2022
• RSeQC
  ...put sequence data especially RNA-seq data. “Basic modules” quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while “RNA-se
  3 KB (328 words) - 17:48, 10 June 2022
• Barrnap
  ...more CPUs. Running time is approximately 1 second per 1 megabase of input sequence.
  3 KB (328 words) - 17:55, 10 June 2022
• ProtExcluder
  ...ude the portion of DNA sequence (as well as certain length of the flanking sequence – given by the user, default = 50 bp) matching subjects in a protein data
  3 KB (329 words) - 21:22, 6 December 2019
• Bridger
  ...r to search an optimal set of paths (transcripts) that can be supported by sequence data and could explain all observed splicing events of each locus.
  3 KB (341 words) - 13:14, 15 August 2022
• Last
  * Handle big sequence data, e.g: * Use sequence quality data properly.
  3 KB (342 words) - 19:29, 12 August 2022
• Probalign
  ...terior probability estimates to compute maximum expected accuracy multiple sequence alignments. It performs statistically significantly better than the leading generation and manipulation of multiple sequence alignments using
  3 KB (349 words) - 19:36, 21 August 2022
• CGView
  ...w sequence features, gene and protein names, COG category assignments, and sequence composition characteristics. CCT can generate maps in a variety of sizes, i
  3 KB (351 words) - 19:39, 23 May 2022
• PhyloPhlAn2
  ...nction that selects how many position to consider for each of the multiple-sequence alignment.
  3 KB (375 words) - 17:57, 9 June 2022
• Jasper
  ...assemblies. JASPER is substantially faster than polishing methods based on sequence alignment, and more accurate than currently available k-mer based methods.
  3 KB (354 words) - 16:42, 14 December 2023
• EMBOSS
  ...BOSS also integrates a range of currently available packages and tools for sequence analysis into a seamless whole. EMBOSS breaks the historical trend towards
  3 KB (372 words) - 15:01, 15 August 2022
• SeqPrep
  ...most cases) so they are forcefully merged. When reads do not have adapter sequence they must be treated with care when doing the merging, so a much more sensi
  3 KB (371 words) - 22:38, 21 August 2022
• HybPiper
  HybPiper was designed for targeted sequence capture, in which DNA sequencing libraries are enriched for gene regions of ...., Zerega, N. J. C, and Wickett, N. J. (2016). HybPiper: Extracting Coding Sequence and Introns for Phylogenetics from High-Throughput Sequencing Reads Using T
  3 KB (349 words) - 18:36, 10 June 2022
• Maq
  Follow these steps to run Maq. All you need is a reference sequence file in the FASTA format. Prepare a reference sequence (ref.fasta), better a bacterial genome to make the test run faster.
  3 KB (377 words) - 19:47, 12 August 2022
• Viralmsa
  ViralMSA is a tool to perform reference-guided multiple sequence alignment of viral genomes. ViralMSA wraps around existing read mapping too ...Moshiri N (2020). "ViralMSA: Massively scalable reference-guided multiple sequence alignment of viral genomes." Bioinformatics. btaa743. doi:10.1093/bioinform
  3 KB (357 words) - 19:56, 27 May 2022
• MODELLER
  ...alignment of protein sequences and/or structures, clustering, searching of sequence databases, comparison of protein structures, etc. MODELLER is available for
  3 KB (364 words) - 19:53, 12 August 2022
• Trim Galore
  ...h some added functionality to remove biased methylation positions for RRBS sequence files (for directional, non-directional (or paired-end) sequencing). It's m ...suitable for both ends of paired-end libraries), but accepts other adapter sequence, too
  4 KB (512 words) - 20:52, 12 August 2022
• RDnaTools
  ...is a python package of tools and pipelines for working with ribosomal DNA sequence data generated with the PacBio(R) SMRT sequencing. rDnaTools works by wrapp ...al Ecology community, and their existing tools for analyzing ribosomal DNA sequence data. Since the core of the analyses wrapped by rDnaTools come from the Mot
  3 KB (361 words) - 21:24, 6 December 2019
• Ssr pipeline
  ...quality standards, (2) align paired-end reads into a single composite DNA sequence, and (3) identify sequences that possess microsatellites conforming to user ...n of microsatellite sequences from paired-end Illumina High-Throughput DNA sequence data (ver. 1.1, February 2014): U.S. Geological Survey Data Series 778.
  4 KB (501 words) - 18:55, 6 June 2022
• Quake
  ..., which create false sequence unsimilar to anything in the original genome sequence from which the read was taken.
  3 KB (367 words) - 18:50, 10 June 2022
• Mvftools
  ...e data is encoded based on the information content at a particular aligned sequence site. This contextual encoding allows for rapid computation of phylogenetic
  3 KB (370 words) - 13:58, 30 April 2020
• Erpin
  ...write complex descriptors before starting a search. Instead ERPIN reads a sequence alignement and secondary structure, and automatically infers a statistical ...ert A. (2001) Direct RNA Motif Definition and Identification from Multiple Sequence Alignments using Secondary Structure Profiles. J Mol Biol. 313:1003-11]
  3 KB (377 words) - 21:21, 6 December 2019
• Samtools
  ...nce Alignment/Map) format is a generic format for storing large nucleotide sequence alignments. SAM Tools provide various utilities for manipulating alignments
  3 KB (357 words) - 22:04, 21 August 2022
• BiG-SCAPE
  ...ed on a comparison of their protein domain content, order, copy number and sequence identity.
  3 KB (377 words) - 12:53, 15 August 2022
• PROVEAN
  PROVEAN is useful for filtering sequence variants to identify nonsynonymous or indel variants that are predicted to A fast computation approach to obtain pairwise sequence alignment scores enabled the generation of precomputed PROVEAN predictions
  3 KB (350 words) - 20:27, 12 August 2022
• MACH
  available genotype and shotgun sequence data to estimate unobserved Li Y, Willer CJ, Ding J, Scheet P and Abecasis GR (2010) MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes. Genet Ep
  3 KB (363 words) - 20:23, 15 August 2022
• Anchorwave
  ...ragments, i.e., anchor and inter-anchor intervals. By performing sensitive sequence alignment for each shorter interval via a 2-piece affine gap cost strategy ...Michelle C. Stitzer. AnchorWave: Sensitive alignment of genomes with high sequence diversity, extensive structural polymorphism, and whole-genome duplication.
  3 KB (367 words) - 21:10, 20 September 2023
• FastANI
  ...avoids expensive sequence alignments and uses Mashmap as its MinHash based sequence mapping engine to compute the orthologous mappings and alignment identity e
  3 KB (380 words) - 21:21, 6 December 2019
• ShapeMapper
  ...grates careful handling of all classes of adduct-induced sequence changes, sequence variant correction, basecall quality filters, and quality-control warnings
  3 KB (387 words) - 21:24, 6 December 2019
• INDELible
  INDELible is a new, portable, and flexible application for biological sequence simulation that combines many features in the same place for the first time ...tcher, W. and Yang, Z. 2009. INDELible: a flexible simulator of biological sequence evolution. Mol. Biol. and Evol. 2009 26(8):1879-1888]
  3 KB (384 words) - 13:34, 28 June 2021
• MOSAIK
  ...ikSort resolves paired-end reads and sorts the alignments by the reference sequence coordinates. Finally, MosaikText converts alignments to different text-base
  3 KB (414 words) - 11:59, 19 August 2022
• Ncbi-vdb
  ...sion by Reference, which only stores the differences in base pairs between sequence data and the segment it aligns to. The process to restore original data, fo
  3 KB (428 words) - 14:33, 19 August 2022
• Scrappie
  * scrappie squiggle Create approximate squiggle for sequence * scrappie seqmappy Map signal to sequence via basecall posteriors
  3 KB (416 words) - 13:43, 7 April 2021
• TWINSCAN
  with the length of the target sequence. A rough guideline is 1 GB of memory for 1 Mb of input sequence.
  3 KB (386 words) - 20:20, 27 May 2022
• TRF
  ...Repeats with pattern size in the range from 1 to 2000 bases are detected. Sequence information sent to the server is confidential and deleted after program ex
  3 KB (442 words) - 20:52, 12 August 2022
• SCRATCH-1D
  * EVALpro release 1.0 (2019) : Evaluation of sequence-based & profile-based predictors * PROFILpro release 2.0 (2021) : Protein evolutionary information / sequence profiles
  3 KB (381 words) - 20:35, 12 August 2022

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