Debian Med Biology packages

 - The slab position and thickness are visible in a small window.
 - Atomic bonds as well as atoms are treated as independent drawable
   objects.
 - The atomic and bond colors depend on position. Five mapping modes
   are available (as for slab).
 - Capable to display stereo image.
 - Capable to display other geometric objects, like membrane.
 - Atomic information is available for atom covered by the mouse
   pointer. No click required, just move the mouse pointer over the
   structure!
 - Capable to load more than one structure.
 - Capable to draw Ramachandran plot, helical wheel, Venn diagram,
   averaged hydrophobicity and hydrophobic moment plot.
 - The command prompt is available at the bottom of the main window.
   It is able to display one error message and one command string.

 * Comprehensive alignment plots for any GFF-feature. Attributes are defined
   separately so you can modify only whatsoever attributes for a given file or
   share same customization across different data-sets.
 * All parameters are set by default within the program, but it can be also
   fully configured via gff2ps-like flexible customization files. Program can
   handle several of such files, summarizing all the settings before producing
   the corresponding figure. Moreover, all customization parameters can be set
   via command-line switches, which allows users to play with those parameters
   before adding any to a customization file.
 * Source order is taken from input files, if you swap file order you can
   visualize alignment and its annotation with the new input arrangement.
 * All alignment scores can be visualized in a PiP box below gff2aplot area,
   using grey-color scale, user-defined color scale or score-dependent
   gradients.
 * Scalable fonts, which can also be chosen among the basic PostScript default
   fonts. Feature and group labels can be rotated to improve readability in
   both annotation axes.
 * The program is still defined as a Unix filter so it can handle data from
   files, redirections and pipes, writing output to standard-output and
   warnings to standard error.
 * gff2aplot is able to manage many physical page formats (from A0 to A10, and
   more -see available page sizes in its manual-), including user-defined ones.
   This allows, for instance, the generation of poster size genomic maps, or
   the use of a continuous-paper supporting plotting device, either in portrait
   or landscape.
 * You can draw different alignments on same alignment plot and distinguish
   them by using different colors for each.
 * Shape dictionary has been expanded, so that further feature shapes are now
   available (see manual).
 * Annotation projections through alignment plots (so called ribbons) emulate
   transparencies via complementary color fill patterns. This feature allows
   to show color pseudo-blending when horizontal and vertical ribbons overlap.

 glam2:       discovering motifs shared by a set of sequences;
 glam2scan:   finding matches, in a sequence database, to a motif discovered
              by glam2;
 glam2format: converting glam2 motifs to  standard alignment formats;
 glam2mask:   masking glam2 motifs out of sequences, so that weaker motifs
              can be found;
 glam2-purge: removing highly similar members of a set of sequences.

 - Fast align Illumina/SOLiD reads to the reference genome. With the
   default options, one million pairs of reads can be mapped to the
   human genome in about 10 CPU hours with less than 1G memory.
 - Accurately measure the error probability of the alignment of each
   individual read.
 - Call the consensus genotypes, including homozygous and heterozygous
   polymorphisms, with a Phred probabilistic quality assigned to each base.
 - Find short indels with paired end reads.
 - Accurately find large scale genomic deletions and translocations with
   paired end reads.
 - Discover potential CNVs by checking read depth.
 - Evaluate the accuracy of raw base qualities from sequencers and help
   to check the systematic errors.

 - Do de novo assembly. (Maq can only call the consensus by mapping reads
   to a known reference.)
 - Map shorts reads against themselves. (Maq can only find complete overlap
   between reads.)
 - Align capillary reads or 454 reads to the reference. (Maq cannot align
   reads longer than 63bp.)

 * allow for exchange of PCR data between researchers/laboratories
 * enable traceability of the data
 * prevent problems when submitting data to dbSTS or dbSNP
 * enable the writing of standard scripts to extract data (e.g. a
   list of PCR primers, SNP positions or haplotypes for different animals)

 NucML:  Maximum Likelihood Inference of Nucleic Acid Phylogeny
 ProtST: Basic Statistics of Protein Sequences
 NucST:  Basic Statistics of Nucleic Acid Sequences
 NJdist: Neighbor Joining Phylogeny from Distance Matrix

 mollist:  get identifiers list        molrev:   reverse DNA sequences
 molcat:   concatenate sequences       molcut:   get partial sequences
 molmerge: merge sequences             nuc2ptn:  DNA -> Amino acid
 rminsdel: remove INS/DEL sites        molcodon: get specified codon sites
 molinfo:  get varied sites            mol2mol:  MOLPHY format beautifer
 inl2mol:  Interleaved -> MOLPHY       mol2inl:  MOLPHY -> Interleaved
 mol2phy:  MOLPHY -> Sequential        phy2mol:  Sequential -> MOLPHY
 must2mol: MUST -> MOLPHY              etc.

 * Translation of a nucleotide sequence;
 * Blast search (eg. blastn, blastp etc.) of the desired nucleotide/protein
   sequence;
 * Calculation of properties (like PI, charge, molecular weight, AT/GC content
   etc.) of a protein/nucleotide sequence;
 * Conversion between formats (Genbank, Fasta, Swiss-Prot etc.);
 * Prediction of sequence for sub-cellular localization (PREDOTAR, TargetP,
   pSORT etc).

 * Visualization of molecules, molecular trajectories and surfaces
   of crystallography data or orbitals
 * Molecular builder and sculptor
 * Internal raytracer and movie generator
 * Fully extensible and scriptable via a python interface

 * speed improvement;
 * allow large, chromosome scale, DNA sequences to be used;
 * provide more detailed output about splice types;
 * provide more detailed output about polyA sites;
 * misc code cleanups and fixes.