Debian-Med micro-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. 

 * 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). 

 Homepage: http://rasmol.org 

 * 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. 

 * E-Cell Simulation Environment (or E-Cell SE) 
 * E-Cell Modeling Environment (or E-Cell ME) 
 * E-Cell Analysis Toolkit. 

 * Simultaneous bird's eye and detailed views of the genome. 
 * Scroll, zoom, center. 
 * Attach arbitrary URLs to any annotation. 
 * Order and appearance of tracks are customizable by administrator and end-user. 
 * Search by annotation ID, name, or comment. 
 * Supports third party annotation using GFF formats. 
 * Settings persist across sessions. 
 * DNA and GFF dumps. 
 * Connectivity to different databases, including BioSQL and Chado. 
 * Multi-language support. 
 * Third-party feature loading. 
 * Customizable plug-in architecture (e.g. run BLAST, dump & import many formats, 
   find oligonucleotides, design primers, create restriction maps, edit features) 

 E. P. Nawrocki, S. R. Eddy. PLoS Comput. Biol., 3:e56, 2007. 

 * The JmolApplet is a web browser applet that can be integrated into web pages. 
 * The Jmol application is a standalone Java application that runs on the 
   desktop. 
 * The JmolViewer is a development tool kit that can be integrated into other 
   Java applications. 

 * exteremely fast (17 CPU hours for whole Human x Mouse genome (with 
   40 nodes: 52 wall minutes)) 
 * scalable (Arbitrarily parallelizable across multiple nodes using MPI. 
   Even a single node with 16GB of ram can handle over 1Gbp of sequence.) 
 * unlimited pattern length 
 * repeat tolerant 
 * intelligent noise reduction