# The FreeBSD Ports Collection ("biology")

You are now in the directory "biology".

This is the one-line description for this category:

Biology

Here are the one-line descriptions for each items in this directory:

    L-Breeder-1.0: Allows you to display and breed L-system forms
    act-2.0: A DNA sequence comparison viewer based on Artemis
    artemis-4.0: A DNA sequence viewer and annotation tool
    avida-1.6.0: Avida is an auto-adaptive genetic system designed for ALife research
    babel-1.6_3: Converts among various molecular file formats
    biojava-1.01: Open-source java tools for processing biological data
    chemeq-1.10_1: Outputs LaTeX code for chemical reaction
    clustalw-1.83: CLUSTAL W Multiple Sequence Alignment Program
    coalesce-1.50: A program to fit population models
    crimap-2.4: Creation of multilocus linkage maps
    deft-2.2_2: Density functional molecular orbital calculation
    distribfold-0.1.20030425: distributedfolding.org distributed protein folding project
    dna-qc-1993.07.26: A quality control algorithm for DNA sequencing projects
    emboss-2.4.1_2: A collection of open source tools for genetic sequence analysis
    fasta-20.u66: A collection of programs for searching DNA and protein databases
    fasta3-33.t08.d4: A collection of programs for searching DNA and protein databases, v3
    fastdnaml-1.2.2: Faster DNAML, makes phylogenetic trees using maximum likelihood
    flip-2.0.2: Flip is used to find/translate orfs
    fluctuate-1.30: A program to fit population models
    garlic-1.4: Molecular viewer, editor and visualization program
    genpak-0.26_2: A set of small utilities to manipulate DNA sequences
    gff2ps-0.97b: Converts gff-formated genomic data-sets to PostScript
    gperiodic-2.0.7: Displays a periodic table of the elements
    grappa-1.0.3: Genome Rearrangements Analysis and Phylogeny Software
    hmmer-2.2.g_1: Profile hidden Markov models for biological sequence analysis
    kinemage-5.79: A molecular visualization program with special functions
    lamarc-2001.08.06: A package of programs for computing population parameters
    libgenome-0.5.2: Toolkit for developing bioinformatic related software in C++
    lsysexp-0.67: A GTK based program for viewing and creating L-system fractals
    migrate-1.2.4: A program to estimate population sizes and migration rates
    molden-3.9: Display molecular orbitals and electron densities in 2D and 3D
    mopac-7.02: Semi-empirical (MNDO, etc.) molecular orbital calculation
    nab-4.5.2: "This is nab (nucleic acid builder), a language for macromolecules"
    ncbi-toolkit-2003.04.21: NCBI development toolkit, including BLAST 2 and GenBank/Entrez support
    nclever-4.0: NClever is a character-based version of NCBI's Entrez program
    ortep3-1.0.3_2: The Oak Ridge Thermal Ellipsoid Plot Program for Crystal Structure
    p5-AcePerl-1.83: Perl5 interface to the ACEDB genome database system
    p5-bioperl-0.7.2: A collection of Perl modules for bioinformatics
    paml-3.13: Phylogenetic Analysis by Maximum Likelihood (PAML)
    phylip-3.6.a3: A Phylogeny Inference Package
    platon-2001.03.09_1: Tool for viewing molecular/crystallographic structures
    povchem-1.0_2: Simple yet powerful tool to generate POV from a PDB file
    primer3-0.9: Primer3 helps to choose primers for PCR reactions
    psi88-1.0: Plotting wavefunctions (molecular orbitals) in 3D
    py23-biopython-1.00.a4: A collection of Python modules for bioinformatics
    pymol-0.90: Free and Open-Source molecular modeling system
    rasmol-2.7.2_1: Fast Molecular Visualization Program
    recombine-1.40: A program to fit population models across sites
    ruby-bio-0.5.3: Integrated environment for Bioinformatics written in Ruby
    seaview-2003.11.17: Multiple DNA/protein sequence alignment editor
    seqio-1.2.2: A set of C functions which can read/write biological sequence files
    sim4-2002.03.03: An algorithm for aligning expressed DNA with genomic sequences
    spdbv-3.7: Deep View Swiss-PdbViewer is a Protein viewer and analysis tool
    tRNAscan-SE-1.21: An improved tool for transfer RNA detection
    t_coffee-1.37: A multiple DNA or protein sequence alignment package
    tinker-4.1: A general purpose molecular modelling package
    treepuzzle-5.1: Maximum likelihood phylogeny reconstruction using quartets
    treeviewx-0.3_1: A phylogenetic tree viewer
    wise-2.2.0: Intelligent algorithms for DNA searches
    xdrawchem-1.7.3: Chemical drawing program
    xmolwt-0.7: Calculate formula weight and percent of each element for a given formula

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