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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>
=================================================================
THE TOOLS
---------
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
------------
Briefly, the shell commands `./configure; make; make install' should configure,
build, and install this package on Linux, Mac OS X or Windows (under
Cygwin). See the platform-specific INSTALL.xxx files for more details.
You can also install SeqTools using a virtual machine (VM) program such as
VirtualBox. Instructions for how to do this using VirtualBox are in INSTALL.VM.
USAGE
-----
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.
Note that you need to have XQuartz or X11 running to run GTK programs on a
Mac. These may be installed by default on your machine. If not, you can download
XQuartz from here: https://www.xquartz.org/
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