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• 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

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