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.

Availability

Version 4.30

Licence

GNU General Public License

Use

module add seqtools-4.30
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

Program manager

meta@cesnet.cz

Homepage

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