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• Category:Alignment
  Biological sequence alignment tools and documentation
  24 members (0 subcategories, 0 files) - 15:24, 23 August 2022
• WebLogo
  WebLogo is an application designed to make the generation of sequence logos as easy and painless as possible. ...precise description of, for example,a binding site, than would a consensus sequence.
  3 KB (417 words) - 17:40, 22 August 2022
• Category:Assembly
  Short Sequence Assembly software.
  20 members (0 subcategories, 0 files) - 15:24, 23 August 2022
• Infernal
  Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases for RNA structure and sequence similarities. It is an implementation of a
  3 KB (305 words) - 19:31, 24 August 2022
• EvoLSTM
  ...robabilities. EvoLSTM brings modern machine-learning approaches to bear on sequence evolution. It will serve as a useful tool to study and simulate complex mut
  3 KB (309 words) - 18:52, 12 August 2022
• Sim4
  ...verlaps the end of the other). If seqfile2 is a database of sequences, the sequence in seqfile1 will be aligned with each of the sequences in seqfile2.
  2 KB (302 words) - 20:41, 12 August 2022
• RNAsalsa
  ...e, that RNAsalsa uses structure information for adjusting and refining the sequence alignment and vice versa.
  3 KB (368 words) - 21:24, 6 December 2019
• Spruceup
  ...ts (alignment rows), which is different from the problem of poorly aligned sequence blocks (alignment columns) commonly addressed by alignment trimming softwar ...identification, visualization, and removal of outliers from large multiple sequence alignments. Journal of Open Source Software, 4(42), 1635, https://doi.org/1
  3 KB (317 words) - 21:24, 6 December 2019
• CD-HIT
  ...-hit produces a set of closely related protein families from a given fasta sequence database.
  3 KB (354 words) - 18:24, 12 August 2022
• SuperCRUNCH
  ...orking with phylogenetic datasets. SuperCRUNCH can be run using any set of sequence data, as long as sequences are in fasta format with standard naming convent ...s (adjust sequence directions, adjust reading frames), several options for sequence alignment (Clustal-O, MAFFT, Muscle, MACSE), and multiple options for align
  4 KB (499 words) - 14:47, 11 May 2020
• RepeatMasker
  sequence as well as a modified version of the query sequence in which On average, almost 50% of a human genomic DNA sequence currently will
  2 KB (325 words) - 20:32, 12 August 2022
• Minigraph
  ...graph constructor. It finds approximate locations of a query sequence in a sequence graph and incrementally augments an existing graph with long query subseque
  2 KB (279 words) - 18:08, 31 March 2021
• Sputnik
  ...the resulting hits are written to stdout along with their position in the sequence, length, and a score determined by the length of the repeat and the number
  2 KB (311 words) - 15:50, 22 August 2022
• FAST
  ...BioPerl FastA format). FAST tools expose the power of Perl and BioPerl for sequence analysis to non-programmers in an easy-to-learn command-line paradigm.
  3 KB (358 words) - 21:21, 6 December 2019
• Artemis
  ...next generation data and the results of analyses within the context of the sequence, and also its six-frame translation. ...: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data.
  3 KB (378 words) - 14:53, 12 August 2022
• Mlstcheck
  ...for each locus, and the ST (or nearest ST), the other contains the genomic sequence for each allele. ...us, the contaminated flag is set. Optionally you can output a concatenated sequence in FASTA format, which you can then use with tree building programs. New, u
  3 KB (395 words) - 18:06, 27 May 2022
• TNTBLAST
  ...ideally) match experimental PCR results. To enable searching of very large sequence databases (i.e. all of Genbank), ThermonucleotideBLAST can use run-time dat
  3 KB (385 words) - 20:08, 2 June 2022
• Seq crumbs
  seq_crumbs aims to be a collection of small sequence processing utilities. ...and most of them take a sequence file as input and create a new processed sequence file as output. This design encourages the assembly of the seq_crumbs utili
  3 KB (328 words) - 15:12, 27 May 2022
• HMMER
  HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods
  3 KB (397 words) - 18:18, 15 August 2022
• Impg
  impg (Implicit Pangenome Graph) projects sequence ranges through many-way (e.g. all-vs-all) pairwise alignments built by tool ...htforward to use to extract FASTA sequences for downstream use in multiple sequence alignment (like mafft) or pangenome graph building (e.g., pggb or minigraph
  3 KB (392 words) - 21:22, 10 April 2024

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