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The fourth is a great example of how interactive graphical tools enable a worker involved in sequence analysis to conveniently execute a variety if different computational tools to explore an alignment's phylogenetic implications; or, to predict the structure and functional properties of a specific sequence, e.g., comparative modelling.
The current FASTA package contains programs for protein:protein, DNA:DNA, protein:translated DNA (with frameshifts), and ordered or unordered peptide searches. Recent versions of the FASTA package include special translated search algorithms that correctly handle frameshift errors (which six-frame-translated searches do not handle very well ...
Combines DNA and Protein alignment, by back translating the protein alignment to DNA. DNA/Protein (special) Local or global: Wernersson and Pedersen: 2003 (newest version 2005) SAGA Sequence alignment by genetic algorithm: Protein: Local or global: C. Notredame et al. 1996 (new version 1998) SAM Hidden Markov model: Protein: Local or global: A ...
QC3 a quality control tool designed for DNA sequencing data for raw data, alignment, and variant calling. qrqc Quickly scans reads and gathers statistics on base and quality frequencies, read length, and frequent sequences. Produces graphical output of statistics for use in quality control pipelines, and an optional HTML quality report.
MNHN-Tree-Tools is an opensource phylogenetics inference software working on nucleic and protein sequences. Clustering of DNA or protein sequences and phylogenetic tree inference from a set of sequences. At the core it employs a distance-density based approach. Thomas Haschka, Loïc Ponger, Christophe Escudé and Julien Mozziconacci [25 ...
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Computational system for predicting protein subchloroplast locations from its primary sequence. It can locate the protein whose subcellular location is chloroplast in one of the four parts: envelope (which consists of outer membrane and inner membrane), thylakoid lumen, stroma and thylakoid membrane. (bio.tools entry) [97]
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