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Free, GPL2 ALLALIGN For DNA, RNA and protein molecules up to 32MB, aligns all sequences of size K or greater, MSA or within a single molecule. Similar alignments are grouped together for analysis. Automatic repetitive sequence filter. Both Local E. Wachtel 2017 Free AMAP: Sequence annealing: Both: Global: A. Schwartz and L. Pachter: 2006: BAli-Phy
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 stochastic optimization approach to maximize the likelihood of the transcript abundances under the observed data.
List of open-source healthcare software; List of biomedical cybernetics software; List of freeware health software; List of genetic engineering software; List of molecular graphics systems; List of systems biology modelling software; Comparison of software for molecular mechanics modeling; List of proprietary bioinformatics software
This page is a subsection of the list of sequence alignment software. Multiple alignment visualization tools typically serve four purposes: Aid general understanding of large-scale DNA or protein alignments; Visualize alignments for figures and publication; Manually edit and curate automatically generated alignments; Analysis in depth
Generates models for unusual DNA, RNA: Free, GPL: New Jersey University: NAnoscale Molecular Dynamics ... List of protein structure prediction software;
TopHat is an open-source bioinformatics tool for the throughput alignment of shotgun cDNA sequencing reads generated by transcriptomics technologies (e.g. RNA-Seq) using Bowtie first and then mapping to a reference genome to discover RNA splice sites de novo. [1] TopHat aligns RNA-Seq reads to mammalian-sized genomes. [2]
FASTA is pronounced "fast A", and stands for "FAST-All", because it works with any alphabet, an extension of the original "FAST-P" (protein) and "FAST-N" (nucleotide) alignment tools. Mappers timeline (since 2001). DNA mappers are plotted in blue, RNA mappers in red, miRNA mappers in green and bisulphite mappers in purple.
Automated software package to annotate eukaryotic genes from RNA-Seq data and associated protein sequences Eukaryotes [1] FragGeneScan: Predicting genes in complete genomes and sequencing Reads: Prokaryotes, Metagenomes [2] ATGpr: Identifies translational initiation sites in cDNA sequences: Human [3] Prodigal