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BioJava is an open-source software project dedicated to provide Java tools to process biological data. [1] [2] [3] BioJava is a set of library functions written in the programming language Java for manipulating sequences, protein structures, file parsers, Common Object Request Broker Architecture (CORBA) interoperability, Distributed Annotation System (DAS), access to AceDB, dynamic ...
BLAST output parsers: MuSeqBox, Zerg, BioParser, BLAST-Explorer, SequenceServer; specialized BLAST-related tools: MEGAN, BLAST2GENE, BOV, Circoletto; Example visualizations of BLAST results are shown in Figure 4 and 5. Fig. 4 Circos-style visualization of BLAST results generated using SequenceServer software.
Stampy is prepared to alignment of reads containing sequence variation like insertions and deletions. It is able to deal with reads up to 4500 bases and presents the output in SAM format. Subread [44] is a read aligner. It uses the seed-and-vote mapping paradigm to determine the mapping location of the read by using its largest mappable region.
The guide tree in the initial versions of Clustal was constructed via a UPGMA cluster analysis of the pairwise alignments, hence the name CLUSTAL. [11] cf. [12] The first four versions of Clustal were numbered using Arabic numerals (1 to 4), whereas the fifth version uses the Roman numeral V. [11] cf. [13] [5] The next two versions proceed alphabetically using the Latin alphabet, with W ...
The name of SAM came from Gabor Marth from University of Utah, who originally had a format under the same name but with a different syntax more similar to a BLAST output. [2] It is widely used for storing data, such as nucleotide sequences, generated by next generation sequencing technologies, and the standard has been broadened to include ...
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The FAST4 format was invented as a derivative of the FASTQ format where each of the 4 bases (A,C,G,T) had separate probabilities stored. It was part of the Swift basecaller, an open source package for primary data analysis on next-gen sequence data "from images to basecalls". The FAST5 format was invented as an extension of the FAST4 format.
Centralized web application that provides data format transformations and facilitates connections with other bioinformatics tools Web browser: LGPL: Broad Institute, collaborative project GENtle: An equivalent to the proprietary Vector NTI, a tool to analyze and edit DNA sequence files Linux, macOS, Windows: GPL: Magnus Manske: gget