Port: babel-1.6 Path: /usr/ports/biology/babel Info: Conversion program among various molecular file formats Maint: frankch@waru.life.nthu.edu.tw Index: biology B-deps: R-deps: Port: biojava-1.01 Path: /usr/ports/biology/biojava Info: Open-source java tools for processing biological data Maint: bio@freebsd.net Index: biology java B-deps: linux-jdk-1.2.2 linux_base-6.1 R-deps: Port: chemeq-1.10 Path: /usr/ports/biology/chemeq Info: Outputs LaTeX code for chemical reaction Maint: rmiya@cc.hirosaki-u.ac.jp Index: biology textproc B-deps: bison-1.28 gettext-0.10.35 R-deps: Port: clustalw-1.81_1 Path: /usr/ports/biology/clustalw Info: CLUSTAL W Multiple Sequence Alignment Program Maint: dbader@eece.unm.edu Index: biology B-deps: R-deps: Port: deft-2.2_1 Path: /usr/ports/biology/deft Info: Density functional molecular orbital calculation Maint: rmiya@cc.hirosaki-u.ac.jp Index: biology B-deps: f2c-2.0.1 f77-0.3 fpp-1.1 R-deps: Port: emboss-1.8.0 Path: /usr/ports/biology/emboss Info: A collection of open source tools for genetic sequence analysis Maint: johann@egenetics.com Index: biology B-deps: XFree86-3.3.6_6 freetype-1.3.1 gd-1.8.3 gettext-0.10.35 gmake-3.79.1 jpeg-6b libtool-1.3.4_1 png-1.0.8_1 R-deps: XFree86-3.3.6_6 freetype-1.3.1 gd-1.8.3 jpeg-6b png-1.0.8_1 Port: fastdnaml-1.2.2 Path: /usr/ports/biology/fastdnaml Info: The faster variant of DNAML, makes phylogenetic trees using maximum likelihood Maint: mzaki@e-mail.ne.jp Index: biology B-deps: gettext-0.10.35 gmake-3.79.1 R-deps: Port: gperiodic-1.2.2 Path: /usr/ports/biology/gperiodic Info: Displays a periodic table of the elements Maint: ports@FreeBSD.org Index: biology B-deps: XFree86-3.3.6_6 gettext-0.10.35 glib-1.2.8 gmake-3.79.1 gtk-1.2.8 R-deps: XFree86-3.3.6_6 gettext-0.10.35 glib-1.2.8 gtk-1.2.8 Port: hmmer-2.1.1 Path: /usr/ports/biology/hmmer Info: Profile hidden Markov models for biological sequence analysis Maint: barnhart@genetics.wustl.edu Index: biology B-deps: R-deps: Port: kinemage-5.79 Path: /usr/ports/biology/kinemage Info: A molecular visualization program with special functions Maint: jeremy@external.org Index: biology B-deps: XFree86-3.3.6_6 open-motif-2.1.30_1 xpm-3.4k R-deps: XFree86-3.3.6_6 open-motif-2.1.30_1 xpm-3.4k Port: molden-3.6_1 Path: /usr/ports/biology/molden Info: Display molecular orbitals and electron densities in 2D and 3D Maint: rmiya@cc.hirosaki-u.ac.jp Index: biology B-deps: R-deps: Port: mopac-7.02 Path: /usr/ports/biology/mopac Info: Semi-empirical (MNDO, etc.) molecular orbital calculation Maint: rmiya@cc.hirosaki-u.ac.jp Index: biology B-deps: f2c-2.0.1 f77-0.3 fpp-1.1 gettext-0.10.35 gmake-3.79.1 R-deps: Port: nab-4.2 Path: /usr/ports/biology/nab Info: This is nab (nucleic acid builder), a language for macromolecules Maint: bdodson@scms.utmb.edu Index: biology B-deps: R-deps: Port: ncbi-toolkit-2000.10.31_1 Path: /usr/ports/biology/ncbi-toolkit Info: National Center for Biotechnology Information (NCBI) Development Toolkit Maint: tony.maher@ebioinformatics.com Index: biology B-deps: XFree86-3.3.6_6 open-motif-2.1.30_1 xpm-3.4k R-deps: XFree86-3.3.6_6 open-motif-2.1.30_1 xpm-3.4k Port: ortep3-1.0.3_2 Path: /usr/ports/biology/ortep3 Info: The Oak Ridge Thermal Ellipsoid Plot Program for Crystal Structure Maint: rmiya@cc.hirosaki-u.ac.jp Index: biology B-deps: R-deps: Port: p5-AcePerl-1.67 Path: /usr/ports/biology/p5-AcePerl Info: Perl interface to the ACEDB genome database system Maint: bio@freebsd.net Index: biology databases perl5 B-deps: R-deps: Port: p5-bioperl-0.6.2 Path: /usr/ports/biology/p5-bioperl Info: A collection of Perl modules for bioinformatics Maint: johann@egenetics.com Index: biology perl5 B-deps: p5-AcePerl-1.67 p5-IO-stringy-1.216 p5-libwww-5.48 R-deps: Port: paml-3.01 Path: /usr/ports/biology/paml Info: Phylogenetic Analysis by Maximum Likelihood (PAML) Maint: dbader@eece.unm.edu Index: biology B-deps: R-deps: Port: phylip-3.5 Path: /usr/ports/biology/phylip Info: A Phylogeny Inference Package Maint: dbader@eece.unm.edu Index: biology B-deps: R-deps: Port: platon-2000.06.05 Path: /usr/ports/biology/platon Info: Tool for viewing molecular/crystallographic structures Maint: rmiya@cc.hirosaki-u.ac.jp Index: biology B-deps: R-deps: Port: povchem-1.0_1 Path: /usr/ports/biology/povchem Info: Simple yet powerful tool to generate POV from a PDB file Maint: frankch@waru.life.nthu.edu.tw Index: biology graphics B-deps: R-deps: Port: psi88-1.0 Path: /usr/ports/biology/psi88 Info: Plotting wavefunctions (molecular orbitals) in 3D Maint: rmiya@cc.hirosaki-u.ac.jp Index: biology B-deps: R-deps: Port: py-biopython-0.90.d03 Path: /usr/ports/biology/py-biopython Info: A collection of Python modules for bioinformatics Maint: johann@egenetics.com Index: biology python B-deps: py-numeric-17.1.2 python-2.0 R-deps: python-2.0 Port: rasmol-2.7.1 Path: /usr/ports/biology/rasmol Info: Fast Molecular Visualization Program Maint: frankch@waru.life.nthu.edu.tw Index: biology B-deps: XFree86-3.3.6_6 R-deps: XFree86-3.3.6_6 Port: seaview-1.0 Path: /usr/ports/biology/seaview Info: Multiple DNA sequence alignment editor Maint: frankch@waru.life.nthu.edu.tw Index: biology B-deps: XFree86-3.3.6_6 xforms-0.89 R-deps: XFree86-3.3.6_6 xforms-0.89 Port: sim4-2000.10.19 Path: /usr/ports/biology/sim4 Info: An algorithm for aligning expressed DNA with genomic sequences Maint: bio@freebsd.net Index: biology B-deps: R-deps: Port: tinker-3.7 Path: /usr/ports/biology/tinker Info: A general purpose molecular modelling package Maint: gjohnson@nola.srrc.usda.gov Index: biology B-deps: R-deps: Port: xdrawchem-0.83 Path: /usr/ports/biology/xdrawchem Info: Chemical drawing program Maint: trevor@FreeBSD.org Index: biology B-deps: Mesa-3.2.1_1 XFree86-3.3.6_6 gettext-0.10.35 gmake-3.79.1 jpeg-6b lcms-1.06 libmng-0.9.3 png-1.0.8_1 qt-2.2.3 R-deps: Mesa-3.2.1_1 XFree86-3.3.6_6 jpeg-6b lcms-1.06 libmng-0.9.3 png-1.0.8_1 qt-2.2.3 Port: xmolwt-0.3 Path: /usr/ports/biology/xmolwt Info: Calculate formula weight and percent of each element for a given formula Maint: rmiya@cc.hirosaki-u.ac.jp Index: biology B-deps: XFree86-3.3.6_6 gettext-0.10.35 glib-1.2.8 gmake-3.79.1 gtk-1.2.8 R-deps: XFree86-3.3.6_6 gettext-0.10.35 glib-1.2.8 gtk-1.2.8 Port: py-martel-0.4_1,1 Path: /usr/ports/textproc/py-martel Info: A parser generator for regular languages, written in Python Maint: johann@egenetics.com Index: textproc biology python B-deps: python-2.0 R-deps: py-mxTextTools-1.1.1 python-2.0