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PHP language toolkit with classes for DNA and protein sequence analysis, alignment, database parsing, and other bioinformatics tools Cross-platform: GPL v2 Open Bioinformatics Foundation: Biopython: Python language toolkit Cross-platform: Biopython [2] Open Bioinformatics Foundation: BioRuby: Ruby language toolkit Linux, macOS, Windows [3] GPL ...
[10] After importing a dataset, MEGA provides multiple different data viewer options. For example, users can view statistical attributes and select subsets in the Sequence Data Explorer or use the Distance Data Explorer to inspect pairwise distance data. [11] Another feature of MEGA is the visual specification of domain groups.
SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM (Sequence Alignment/Map), BAM (Binary Alignment/Map) and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA.
Sequence Alignment Map (SAM) is a text-based format originally for storing biological sequences aligned to a reference sequence developed by Heng Li and Bob Handsaker et al. [1] It was developed when the 1000 Genomes Project wanted to move away from the MAQ mapper format and decided to design a new format.
DNADynamo is a commercial DNA sequence analysis software package produced by Blue Tractor Software Ltd [1] that runs on Microsoft Windows, Mac OS X and Linux [2] It is used by molecular biologists [3] to analyze DNA and Protein sequences. A free demo is available from the software developers website.
Alignment-free methods can broadly be classified into five categories: a) methods based on k-mer/word frequency, b) methods based on the length of common substrings, c) methods based on the number of (spaced) word matches, d) methods based on micro-alignments, e) methods based on information theory and f) methods based on graphical representation.
A notable difference is the fact that GENSCAN utilizes a genomic sequence model that exclusively focuses double-stranded DNA where genes that are present on both strands are simultaneously analyzed. Also, GENSCAN is capable of analyzing genomes in situations where there are partial genes or no genes, rather than only being able to analyze ...
The method plots data points that represent a specific time and fluorescence intensity at various wavelengths of light to represent a DNA profile. [ 2 ] [ page needed ] In the field of genetics, an electropherogram is a plot of DNA fragment sizes, typically used for genotyping such as DNA sequencing . [ 3 ]