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WELCOME TO THE SEQTOOLS PACKAGE

This package is aimed at those involved in genome annotation 
and contains tools for detailed analysis of sequences/alignments.

Homepage: www.sanger.ac.uk/resources/software/seqtools/
Author:   Gemma Barson <gemma.barson@sanger.ac.uk>

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THE TOOLS
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blixem - 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.

blixemh - the same as blixem but with additional functionality for fetching sequences via HTTP (currently only supported for authorised users).

dotter - 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 - 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. 


INSTALLATION
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See the INSTALL file.


USAGE
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Run the individual programs without arguments to see their usage information, or view the documentation from this folder: doc/User_doc/index.html.

Help pages can also be accessed from within the programs using the 'Help' menu, the lifebuoy icon on the toolbar or the Ctrl-H shortcut key.

Sample data and examples can be found in the 'examples' directory.