16:48 aaron 

Adding port biology/p5-Bio-Phylo, Phylogenetic analysis using perl.

Approved by:    tobez (implicit)

20:09 ehaupt 

Add protomol 2.0.3, OO, component based, framework for molecular
dynamics (MD) simulations.

PR:             95123
Submitted by:   Sangwoo Shim <sangwoos@gmail.com>

21:31 garga 

Bioperl-run contain modules that provides a PERL interface to various
bioinformatics applications. This allows various applications to be used
with common Bioperl objects.

WWW: http://bioperl.org/

PR:             ports/93675
Submitted by:   Mauricio Herrera Cuadra <mauricio@arareko.net>

21:30 garga 

Bioperl-run contain modules that provides a PERL interface to various
bioinformatics applications. This allows various applications to be used
with common Bioperl objects.

WWW: http://bioperl.org/

PR:             ports/93674
Submitted by:   Mauricio Herrera Cuadra <mauricio@arareko.net>

22:31 garga 

Add lagan 1.2, efficient tools for large-scale multiple alignments of
genomic DNA.

PR:             ports/93058
Submitted by:   Fernan Aguero <fernan@iib.unsam.edu.ar>

10:41 garga 

Add mafft 5.734, multiple sequence alignments based on fast Fourier
transform.

PR:             ports/93059
Submitted by:   Fernan Aguero <fernan@iib.unsam.edu.ar>

10:35 garga 

Add dotter 20021204 # last modified date in FTP server, a viewer for
multiple sequence alignments.

PR:             ports/93055
Submitted by:   Fernan Aguero <fernan@iib.unsam.edu.ar>

10:26 garga 

Add blat 33, a fast tool for local sequence similarity searches.

PR:             ports/93060
Submitted by:   Fernan Aguero <fernan@iib.unsam.edu.ar>

10:24 garga 

Add belvu 2.29, a viewer for multiple sequence alignments.

PR:             ports/93056
Submitted by:   Fernan Aguero <fernan@iib.unsam.edu.ar>

09:42 hq 

Jalview is a multiple alignment editor written in Java. It is used widely in a
variety of web pages (e.g. the EBI Clustalw server and the Pfam protein domain
database) and is also available as a general purpose alignment editor.

WWW: http://www.jalview.org

PR:             93054
Submitted by:   Fernan Aguero <fernan@iib.unsam.edu.ar>

19:47 danfe 

- Resurrect, update to version 1.5 (literally 1.50 since I wanted to avoid
  unnecessary PORTEPOCH bump)
- Update MASTER_SITES and WWW line, provide backup download site
- Come up with better port description
- Reset maintainer to ports@
- Uphold CXX and CXXFLAGS
- Clean up Makefile slightly
- Don't install yet another copy of GPL and texts in French
- Add SHA256 hash to distinfo

21:15 pav 

- Remove expired ports

21:40 barner 

- Re-add p5-bioperl-devel, development version of biology/p5-bioperl
  (A collection of Perl modules for bioinformatics)

PR:             ports/89497
Submitted by:   Mauricio Herrera Cuadra <arareko@yahoo.com>

09:07 kris 

Remove expired ports

20:09 ehaupt 

Add p5-Bio-ASN1-EntrezGene, a Regular expression-based Perl Parser for
NCBI Entrez Gene.

PR:             87423
Submitted by:   Mauricio Herrera Cuadra <mauricio@arareko.net>
Approved by:    novel (mentor) (implicit)

13:09 garga 

Add p5-Bio-Das 1.02, client-side library for Distributed Genome
Annotation System.

PR:             ports/76379
Submitted by:   Razi Khaja <razi@genet.sickkids.on.ca>

08:07 sem 

- biology/act is redundant after biology/artemis update

PR:             ports/76217
Submitted by:   Fernan Aguero <fernan@iib.unsam.edu.ar>
Approved by:    maintainer timeout (2 monthes)

21:16 thierry 

Add finchtv 1.3.0, a chromatogram trace viewer.

PR:             70271
Submitted by:   Fernan Aguero <fernan (at) iib.unsam.edu.ar>

23:44 kris 

As previously announced, remove ports that have reached their expiry date,
and the handful of ports that depended on them.

16:34 sem 

[new port] biology/embassy

PR:             ports/74330
Submitted by:   Fernan Aguero <fernan(at)iib.unsam.edu.ar>

21:35 pav 

Add blast, a powerful software package for gene and protein identification,
using sensitive, selective and rapid similarity searches of protein and
nucleotide sequence databases.

PR:             ports/69636
Submitted by:   Fernan Aguero <fernan@iib.unsam.edu.ar>

14:29 krion 

Add ariadne 1.3, programs to compare protein sequences and
profiles, using the Smith-Waterman algorithm.

PR:             ports/67811
Submitted by:   Fernan Aguero <fernan@iib.unsam.edu.ar>

07:29 kris 

Remove category pkg/COMMENT files in favour of a COMMENT variable in the
category makefile.

Submitted by:   Matthew Seaman <m.seaman@infracaninophile.co.uk>
PR:             59651

02:23 edwin 

new port:biology/lsysexp

        L-system Explorer is a program used for viewing and creating
        L-system fractals.

        The following features are supported:

        - Over 500 builtin L-systems, arranged into about 20 groups.
        - Ability to create and save custom L-systems and L-system groups.
        - Abilty to save images of L-systems (in PNG or JPEG format).
        - Multiple L-systems can be viewed at the same time.
        - Able to use custom colors and gradients.
        - Can also generate random gradients, or completely random colors.
        - Able to draw using lines, points, or a random combination of both.

PR:             iports/51400
Submitted by:   David Yeske <dyeske@yahoo.com>

03:31 kris 

As announced on May 6, remove the broken p5-bioperl-devel port.

06:38 maho 

A new port garlic, free molecular viewer and editor, free molecular
visualization program, protein structure, DNA structure, PDB,
molecular rendering, biological macromolecule.

09:01 kris 

Remove gaussian98

Pointy hat to:  maho

14:22 edwin 

New Port: biology/act

PR:             ports/35753
Submitted by:   Camson Huynh <chuynh@biolateral.com.au>

08:54 ijliao 

add treepuzzle 5.1
Maximum likelihood phylogeny reconstruction using quartets

PR:             45241
Submitted by:   Jan Lentfer <lentferj@neslonek.bio.tu-darmstadt.de>

03:08 lioux 

Connect distribfold to build after moving it from misc category

Prompted by:    kris,
                Adam Weinberger <adam@vectors.cx>,
                Fernan Aguero <fernan@iib.unsam.edu.ar>,
                others

15:31 ijliao 

add primer3 0.9
Primer3 helps to choose primers for PCR reactions

PR:             35298
Submitted by:   Tony Maher <tonym@biolateral.com.au>

14:04 dinoex 

Flip is used to find/translate orfs.
WWW: ftp://megasun.bch.umontreal.ca/pub/flip/
PR:             35332
Submitted by:   tonym@biolateral.com.au

13:58 dinoex 

"Wise2 is package that is focused on comparing DNA sequences at
the level of its conceptual translation, regardless of sequencing
error and introns."

00:01 lioux 

New port L-Breeder version 1.0: Allows you to display and breed
L-system forms

PR:             38725
Submitted by:   David Yeske <dyeske@yahoo.com>

11:53 perky 

Add pymol 0.82, Free and Open-Source molecular modeling system.

PR:             40694
Submitted by:   Nakata Maho <chat95@mbox.kyoto-inet.or.jp>

10:57 ijliao 

add libgenome 0.5.0
Toolkit for developing bioinformatic related software in C++

15:17 ijliao 

add avida 1.6.0
Avida is an auto-adaptive genetic system designed for ALife research

PR:             37268
Submitted by:   Jeremy Karlson <karlj000@unbc.ca>

16:18 dinoex 

Swiss-PdbViewer is an application that provides a user friendly interface
allowing to analyse several proteins at the same time. The proteins can be
superimposed in order to deduce structural alignments and compare their
active sites or any other relevant parts. Amino acid mutations, H-bonds,
angles and distances between atoms are easy to obtain thanks to the
intuitive graphic and menu interface.

Moreover, Swiss-PdbViewer is tightly linked to Swiss-Model, an automated
homology modelling server developped at Glaxo Welcome Experimental Research
in Geneva. Working with these two programs greatly reduces the amount of work
necessary to generate models, as it is possible to thread a protein primary
sequence onto a 3D template and get an immediate feedback of how well the
threaded protein will be accepted by the reference structure before
submitting a request to build missing loops and refine sidechain packing.

Swiss-PdbViewer can also read electron density maps, and provides various
tools to build into the density. In addition, various modelling tools are
integrated and command files for popular energy minimisation packages can be
generated.

Finally, as a special bonus, POV-Ray scenes can be generated from the
current view in order to make stunning ray-traced quality images.

WWW:  http://www.expasy.ch/spdbv/

PR:             33902
Submitted by:   chuynh@biolateral.com.au

14:42 wjv 

Add crimap 2.4, a tool for the creation of multilocus linkage maps.

PR:             35198
Submitted by:   Tony Maher <tonym@biolateral.com.au>

14:18 wjv 

Add tRNAscan-SE 1.21, an improved tool for transfer RNA detection.

PR:             33853
Submitted by:   chuynh@biolateral.com.au