User:Wayne Decatur/Sequence analysis tools
From Proteopedia
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*[http://www.ebi.ac.uk/Tools/muscle/index.html MUSCLE: MUltiple Sequence Comparison by Log-Expectation] | *[http://www.ebi.ac.uk/Tools/muscle/index.html MUSCLE: MUltiple Sequence Comparison by Log-Expectation] | ||
*[http://www.phylosoft.org/archaeopteryx/ Archaeopteryx for the visualization of annotated phylogenetic trees.] | *[http://www.phylosoft.org/archaeopteryx/ Archaeopteryx for the visualization of annotated phylogenetic trees.] | ||
| - | * | + | * [http://www.premierbiosoft.com/netprimer/ Netprimer] |
*[http://www.dyogen.ens.fr/genomicus-60.01/cgi-bin/search.pl 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." ] | *[http://www.dyogen.ens.fr/genomicus-60.01/cgi-bin/search.pl 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." ] | ||
*[https://code.google.com/p/seqtrace/ 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 <nowiki>[</nowiki>contig<nowiki>]</nowiki> 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. | *[https://code.google.com/p/seqtrace/ 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 <nowiki>[</nowiki>contig<nowiki>]</nowiki> 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. | ||
*[http://doua.prabi.fr/software/cap3 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.] | *[http://doua.prabi.fr/software/cap3 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.] | ||
Revision as of 16:24, 25 March 2014
- 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.
