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Source: seqtools
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Andreas Tille <tille@debian.org>
Section: science
Priority: optional
Build-Depends: debhelper-compat (= 13),
libgtk2.0-dev,
libsqlite3-dev,
libcurl4-openssl-dev | libcurl4-dev,
libjsoncpp-dev,
d-shlibs
Standards-Version: 4.5.0
Vcs-Browser: https://salsa.debian.org/med-team/seqtools
Vcs-Git: https://salsa.debian.org/med-team/seqtools.git
Homepage: https://www.sanger.ac.uk/science/tools/seqtools
Rules-Requires-Root: no
Package: libgbtools0
Architecture: any
Multi-Arch: same
Section: libs
Depends: ${shlibs:Depends},
${misc:Depends}
Description: library for visualising sequence alignments
The SeqTools package contains three tools for visualising sequence
alignments: Blixem, Dotter and Belvu.
.
This package contains the library all three tools are linked against.
Package: libgbtools-dev
Architecture: any
Multi-Arch: same
Section: libdevel
Depends: libgbtools0 (= ${binary:Version}),
${devlibs:Depends},
${misc:Depends}
Description: library for visualising sequence alignments (devel)
The SeqTools package contains three tools for visualising sequence
alignments: Blixem, Dotter and Belvu.
.
This package contains the static library and header files.
Package: belvu
Architecture: any
Depends: ${shlibs:Depends},
${misc:Depends}
Breaks: acedb-other-belvu (<< 4.9.39+dfsg.02-2)
Provides: acedb-other-belvu
Replaces: acedb-other-belvu (<< 4.9.39+dfsg.02-2)
Description: multiple sequence alignment viewer and phylogenetic tool
Belvu is a multiple sequence alignment viewer and phylogenetic tool with
an extensive set of user-configurable modes to color residues.
.
* View multiple sequence alignments.
* Residues can be coloured by conservation, with user-configurable
cutoffs and colours.
* Residues can be coloured by residue type (user-configurable).
* Colour schemes can be imported or exported.
* Swissprot (or PIR) entries can be fetched by double clicking.
* The position in the alignment can be easily tracked.
* Manual deletion of rows and columns.
* Automatic editing of rows and columns based on customisable criteria:
- removal of all-gap columns;
- removal of all gaps;
- removal of redundant sequences;
- removal of a column by a user-specified percentage of gaps;
- filtering of sequences by percent identity;
- removal of sequences by a user-specified percentage of gaps;
- removal of partial sequences (those starting or ending with
gaps); and
- removal of columns by conservation (with user-specified
upper/lower cutoffs).
* The alignment can be saved in Stockholm, Selex, MSF or FASTA format.
* Distance matrices between sequences can be generated using a variety
of distance metrics.
* Distance matrices can be imported or exported.
* Phylogenetic trees can be constructed based on various distance-based
tree reconstruction algorithms.
* Trees can be saved in New Hampshire format.
* Belvu can perform bootstrap phylogenetic reconstruction.
Package: blixem
Architecture: any
Depends: ${shlibs:Depends},
${misc:Depends}
Description: interactive browser of sequence alignments
Blixem is an interactive browser of sequence 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.
.
* Overview section showing the positions of genes and alignments around
the alignment window
* Detail section showing the actual alignment of protein or nucleotide
sequences to the genomic DNA sequence.
* View alignments against both strands of the reference sequence.
* View sequences in nucleotide or protein mode; in protein mode, Blixem
will display the three-frame translation of the reference sequence.
* Residues are highlighted in different colours depending on whether
they are an exact match, conserved substitution or mismatch.
* Gapped alignments are supported, with insertions and deletions being
highlighted in the match sequence.
* Matches can be sorted and filtered.
* SNPs and other variations can be highlighted in the reference
sequence.
* Poly(A) tails can be displayed and poly(A) signals highlighted in the
reference sequence.
Package: dotter
Architecture: any
Depends: ${shlibs:Depends},
${misc:Depends}
Breaks: acedb-other-dotter (<< 4.9.39+dfsg.02-2)
Provides: acedb-other-dotter
Replaces: acedb-other-dotter (<< 4.9.39+dfsg.02-2)
Description: detailed comparison of two genomic sequences
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, and a matrix of scores is calculated.
* One sequence is plotted on the x-axis and the other on the y-axis.
* Noise is filtered out so that alignments appear as diagonal lines.
* Pairwise scores are averaged over a sliding window to make the score
matrix more intelligible.
* The averaged score matrix forms a three-dimensional landscape,
with the two sequences in two dimensions and the height of the
peaks in the third. This landscape is projected onto two
dimensions using a grey-scale image - the darker grey of a peak,
the higher the score is.
* The contrast and threshold of the grey-scale image can be adjusted
interactively, without having to recalculate the score matrix.
* An Alignment Tool is provided to examine the sequence alignment that
the grey-scale image represents.
* Known high-scoring pairs can be loaded from a GFF file and overlaid
onto the plot.
* Gene models can be loaded from GFF and displayed alongside the
relevant axis.
* Compare a sequence against itself to find internal repeats.
* Find overlaps between multiple sequences by making a dot-plot of all
sequences versus themselves.
* Run Dotter in batch mode to create large, time-consuming dot-plots as
a background process.
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