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• UFCG
  * '''ufcg train''' generates sequence model of your own fungal marker gene, even from a small set of seed sequenc * '''ufcg align''' conducts multiple sequence alignment of the genes from the set of marker gene profiles.
  3 KB (431 words) - 17:41, 20 September 2023
• Uproc
  ...) toolbox implements a novel algorithm ("Mosaic Matching") for large-scale sequence analysis and is now available in terms of an open source C library. UProC i
  3 KB (418 words) - 20:53, 12 August 2022
• SAMStat
  ...a reference genome in the alignment / map format (SAM/BAM). To monitor the sequence quality over time and to identify problems it is necessary to report variou SAMStat is an efficient C program to quickly display statistics of large sequence files from next generation sequencing projects. When applied to SAM/BAM fil
  3 KB (429 words) - 20:34, 12 August 2022
• Wengan
  alignments can be inferred by building paths on a sequence graph. To achieve this, Wengan builds a new sequence graph called the Synthetic Scaffolding Graph (SSG). The SSG is built from
  4 KB (472 words) - 20:55, 12 August 2022
• BEDTools
  #Calculating the depth and breadth of sequence coverage across defined "windows" in a genome. ...ntrol over how output is reported. Most recently, I have added support for sequence alignments in BAM ([http://samtools.sourceforge.net/]) format, as well as f
  3 KB (485 words) - 12:48, 15 August 2022
• TREEPUZZLE
  ...t computing an overall tree and to visualize the phylogenetic content of a sequence alignment. TREE-PUZZLE also conducts a number of statistical tests on the d
  4 KB (450 words) - 19:31, 10 June 2022
• Sate
  SATé is a software package for inferring a sequence alignment and phylogenetic tree. The iterative algorithm involves repeated .... Linder, T. Warnow, 2009. "Rapid and accurate large scale coestimation of sequence alignments and phylogenetic trees." Science, 324(5934), pp. 1561-1564, 19 J
  7 KB (910 words) - 20:43, 21 December 2022
• BLAT
  sequence. BLAT is much faster than older tools such as BLAST for nucleotide and the genome likely to be similar to the query sequence. It performs an alignment
  3 KB (484 words) - 13:03, 15 August 2022
• Fast-Plast
  ...roximately 30 minutes with no user mediation. In addition to a chloroplast sequence, Fast-Plast identifies chloroplast genes present in the final assembly. .... Lohse, and B. Usadel. 2014. Trimmomatic: A flexible trimmer for Illumina Sequence Data. Bioinformatics, btu170.
  4 KB (487 words) - 21:20, 6 December 2019
• Gffread
  GFF/GTF parsing utility providing format conversions, region filtering, FASTA sequence extraction and more.
  2 KB (242 words) - 19:02, 12 August 2022
• SeCaPr
  A computational pipeline for processing Illumina sequence capture data
  2 KB (246 words) - 21:24, 6 December 2019
• InStruct
  ...subpopulations and classfies each individual into subpopulations given the sequence data.
  2 KB (254 words) - 18:00, 11 March 2020
• BppSuite
  BppSuite is a suite of ready-to-use programs for phylogenetic and sequence analysis.
  2 KB (248 words) - 15:37, 9 December 2022
• Pyfasta
  Fast, memory-efficient, pythonic (and command-line) access to fasta sequence files.
  2 KB (238 words) - 19:58, 21 August 2022
• Randfold
  Randfold compute the probability that, for a given RNA sequence, the Minimum Free Energy (MFE) of the secondary structure is different from
  2 KB (262 words) - 21:29, 21 August 2022
• Staden
  A fully developed set of DNA sequence assembly (Gap4 and Gap5), editing and analysis tools (Spin) for Unix, Linux
  2 KB (254 words) - 15:59, 22 August 2022
• Talesf
  ...sites for transcription activator-like (TAL) effectors in a given genomic sequence.
  2 KB (256 words) - 21:29, 6 December 2019
• Hgtector
  ...-wide detection of putative horizontal gene transfer (HGT) events based on sequence homology search hit distribution statistics.
  2 KB (253 words) - 17:04, 10 October 2022
• GeP
  Genome Profiler (GeP) is a program to perform whole-genome multilocus sequence typing (wgMLST) analysis for bacterial isolates.
  2 KB (255 words) - 15:19, 10 June 2022
• LIGR
  LIGR Assembler is a sequence assembly program. It was derived from TIGR Assembler and addresses some of
  2 KB (249 words) - 19:55, 15 August 2022

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