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In 2004, Affymetrix released IGB as open source software, along with the Genoviz SDK, a graphics library for building genome browser applications. The first release of the code base was done as a compressed file archive. Soon after, the code was imported into a new repository at SourceForge. Since then, all development has proceeded in public ...
Fast detection of coding regions in short genome sequences: Dragon Promoter Finder Program to recognize vertebrate RNA polymerase II promoters: Vertebrates [7] EasyGene: The gene finder is based on a hidden Markov model (HMM) that is automatically estimated for a new genome. Prokaryotes [8] [9] EuGene: Integrative gene finding: Prokaryotes ...
Clustal Omega, ClustalW2, MAFFT, MUSCLE, BioJava are integrated to construct alignment Tree calculation tool calculates phylogenetic tree using BioJava API and lets user draw trees using Archaeopteryx: Software is package of 7 interactive visual tools for multiple sequence alignments. Major focus is manipulating large alignments.
Indexes the genome with periodic seeds to quickly find alignments with full sensitivity up to four mismatches. It can map Illumina and SOLiD reads. Unlike most mapping programs, speed increases for longer read lengths. Yes Free, GPL [49] PRIMEX Indexes the genome with a k-mer lookup table with full sensitivity up to an adjustable number of ...
Strawberry A program for genome-guided transcripts reconstruction and quantification from paired-end RNA-seq. StringTie StringTie is an assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing ...
The agency's traveler-based genomic surveillance program, or TGS, began in 2021 to help with early detection of new SARS-CoV-2 variants. The program includes seven participating international ...