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Alternatively, here is a categorization according to the respective bioinformatics subfield specialized on: Sequence analysis software. List of sequence alignment software. List of alignment visualization software. Alignment-free sequence analysis. De novo sequence assemblers. List of gene prediction software. List of disorder prediction software.
Open Bioinformatics Foundation. BioPHP. 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.
A combination of tools is employed: PALMapper (reads alignment), mTiM and mGene (inference of new transcripts). Salmon is a software tool for computing transcript abundance from RNA-seq data using either an alignment-free (based directly on the raw reads) or an alignment-based (based on pre-computed alignments) approach. It uses an online ...
List of ray tracing software. Ray tracing is a technique that can generate near photo-realistic computer images. A wide range of free software and commercial software is available for producing these images. This article lists notable ray-tracing software. Software.
Constituent amino-acids can be analyzed to predict secondary, tertiary and quaternary protein structure. This list of protein structure prediction software summarizes notable used software tools in protein structure prediction, including homology modeling, protein threading, ab initio methods, secondary structure prediction, and transmembrane helix and signal peptide prediction.
InCroMAP. tool for the integration of omics data and joint visualization of experimental data in pathways. multiplatform (Java-based) LGPL. [14] Pathview. pathway based data integration and visualization, easy to use and integrate into pathway analysis. multiplatform (R/Bioconductor) GPL.
MegAlign Pro (Lasergene Molecular Biology) Software to align DNA, RNA, protein, or DNA + protein sequences via pairwise and multiple sequence alignment algorithms including MUSCLE, Mauve, MAFFT, Clustal Omega, Jotun Hein, Wilbur-Lipman, Martinez Needleman-Wunsch, Lipman-Pearson and Dotplot analysis. Both.
Software is package of 7 interactive visual tools for multiple sequence alignments. Major focus is manipulating large alignments. Includes MSApad, MSA comparator, MSA reconstruction tool, FASTA generator and MSA ID matrix calculator. Clustal W, MSF, PHYLIP, PIR, GDE, Nexus. Proprietary, freeware.