User:Wayne Decatur/Sequence analysis tools

From Proteopedia

• Plasmapper
• Online Schematic plasmid drawing tool
• Online restriction mapper
• NEBcutter
• old web cutter
• Sequence Manipulation Suite: Restriction Map - has at the left side links to other tools they have
• Biotools and EMBOSS at UMASS MED
• MUSCLE: MUltiple Sequence Comparison by Log-Expectation
• Archaeopteryx for the visualization of annotated phylogenetic trees.
• Netprimer
• Genomicus: Genomes in Evolution - "genome browser that enables users to navigate in genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time."

• SeqTrace- "is an application for viewing and processing DNA sequencing chromatograms (trace files). SeqTrace makes it easy to quickly generate high-quality finished sequences from a large number of trace files. SeqTrace can automatically identify, align, and compute [contig] consensus sequences from matching forward and reverse traces, filter low-quality base calls, and perform end trimming of finished sequences. The finished DNA sequences can then be exported to common sequence file formats, such as FASTA. " Written in Python.
• CAP3 Sequence Assembly Program - online, webserver for making contigs from DNA sequences. "form allows you to assemble a set of contiguous sequences (contigs) with the CAP3 program.
• Nucleobytes - DNA editor and 4peaks sequence chromatogram viewer along with other mac software