SeqTools

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Description

A suite of tools for visualising sequence alignments.

Blixem is an interactive browser of pairwise alignments that have been stacked up in a "master-slave" multiple alignment; it is not a 'true' multiple alignment but a 'one-to-many' alignment. It displays an overview section showing the positions of genes and alignments around the alignment window, and a detail section showing the actual alignment of protein or nucleotide sequences to the genomic DNA sequence.

Dotter is a graphical dot-matrix program for detailed comparison of two sequences. Every residue in one sequence is compared to every residue in the other, with one sequence plotted on the x-axis and the other on the y-axis. Noise is filtered out so that alignments appear as diagonal lines.

Belvu is a multiple sequence alignment viewer and phylogenetic tool. It has an extensive set of user-configurable modes to color residues by conservation or by residue type, and some basic alignment editing capabilities. It can generate distance matrices between sequences and construct distance-based trees, either graphically or as part of a phylogenetic software pipeline.

License

GNU General Public License

Usage

Upcoming modulesystem change alert!

Due to large number of applications and their versions it is not practical to keep them explicitly listed at our wiki pages. Therefore an upgrade of modulefiles is underway. A feature of this upgrade will be the existence of default module for every application. This default choice does not need version number and it will load some (usually latest) version.

You can test the new version now by adding a line

source /cvmfs/software.metacentrum.cz/modulefiles/5.1.0/loadmodules

to your script before loading a module. Then, you can list all versions of seqtools and load default version of seqtools as

module avail seqtools/ # list available modules
module load seqtools   # load (default) module


If you wish to keep up to the current system, it is still possible. Simply list all modules by

module avail seqtools

and choose explicit version you want to use. Then run

belvu 
blixem
dotter 

Documentation

https://www.sanger.ac.uk/resources/software/seqtools/#t_doc ftp://ftp.sanger.ac.uk/pub/resources/software/seqtools/Docs/README

Homepage

https://www.sanger.ac.uk/resources/software/seqtools/