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Category listing - biology
Click to add this to your default watch list[s] Software related to biology.- Number of ports in this category: 89

Ports marked with a * actually reside within another category but have biology listed as a secondary category.


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InsightToolkit 2.8.1* search for ports that depend on this port
Insight Toolkit
Maintained by: bacon@smithers.neuro.mcw.edu search for ports maintained by this maintainer
Port Added: 07 Sep 2006 04:14:06
Also Listed In: science
L-Breeder 1.0_10 search for ports that depend on this port
Allows you to display and breed L-system forms
Maintained by: dyeske@gmail.com search for ports maintained by this maintainer
Port Added: 21 Aug 2002 01:02:20
adun 0.8.2 search for ports that depend on this port
Molecular Simulator for GNUstep
Maintained by: dinoex@FreeBSD.org search for ports maintained by this maintainer
Port Added: 09 Nov 2006 20:37:38
Also Listed In: gnustep
afni 2008.01.02.1043* search for ports that depend on this port
Advanced Functional Neuro Imaging
Maintained by: bacon@smithers.neuro.mcw.edu search for ports maintained by this maintainer
Port Added: 25 Jan 2006 17:37:44
Also Listed In: science graphics
ariadne 1.3 search for ports that depend on this port
Programs to compare protein sequences and profiles
Maintained by: fernan@iib.unsam.edu.ar search for ports maintained by this maintainer
Port Added: 22 Jun 2004 15:31:00
artemis 9 search for ports that depend on this port
A DNA sequence viewer and annotation tool
Maintained by: fernan@iib.unsam.edu.ar search for ports maintained by this maintainer
Port Added: 22 Dec 2001 11:39:40
Also Listed In: java
avida 2.4.3 search for ports that depend on this port
Avida is an auto-adaptive genetic system designed for ALife research
Maintained by: sf@slappy.org search for ports maintained by this maintainer
Port Added: 20 Apr 2002 16:17:56
babel 1.6_3 search for ports that depend on this port
Converts among various molecular file formats

There is no maintainer for this port.
Any concerns regarding this port should be directed to the FreeBSD Ports mailing list via ports@FreeBSD.org search for ports maintained by this maintainer
Port Added: unknown
Also Listed In: converters
belvu 2.29 search for ports that depend on this port
A viewer for multiple sequence alignments
Maintained by: fernan@iib.unsam.edu.ar search for ports maintained by this maintainer
Port Added: 15 Mar 2006 10:28:54
biococoa 1.6.0_1 search for ports that depend on this port
Bioinformatics framework
Maintained by: dinoex@FreeBSD.org search for ports maintained by this maintainer
Port Added: 30 Dec 2006 09:21:22
Also Listed In: gnustep
biojava 1.5.b2_1,1 search for ports that depend on this port
Open-source java tools for processing biological data
Maintained by: nemoliu@FreeBSD.org search for ports maintained by this maintainer
Port Added: 10 Oct 2000 09:14:04
Also Listed In: java
blast 2.0_20060322 search for ports that depend on this port
Ignore IGNORE: You must manually fetch wu-blast2 for the FreeBSD platform (blast2.freebsd-6.x-x64.tar.Z) from http://blast.wustl.edu/licensing, place it in /usr/ports/distfiles and then run make again
Restricted RESTRICTED: License does not allow redistribution of binaries. You should first register for the software, which is free for academic use.
WU BLAST, a software package for sequence similarity searches
Maintained by: fernan@iib.unsam.edu.ar search for ports maintained by this maintainer
Port Added: 11 Nov 2004 21:47:25
blat 34 search for ports that depend on this port
A fast tool for local sequence similarity searches
Maintained by: fernan@iib.unsam.edu.ar search for ports maintained by this maintainer
Port Added: 15 Mar 2006 10:29:12
boinc-simap 5.10.5.09_1 search for ports that depend on this port
Similarity Matrix of Proteins project for BOINC
Maintained by: pav@FreeBSD.org search for ports maintained by this maintainer
Port Added: 19 Jun 2006 21:34:29
chemeq 1.50_1 search for ports that depend on this port
Outputs LaTeX code for chemical reaction

There is no maintainer for this port.
Any concerns regarding this port should be directed to the FreeBSD Ports mailing list via ports@FreeBSD.org search for ports maintained by this maintainer
Port Added: 10 Jul 2000 01:14:19
Also Listed In: textproc
clustalw 2.0.6 search for ports that depend on this port
Restricted RESTRICTED: No commercial use.
A multiple alignment program for DNA or proteins
Maintained by: wenheping@gmail.com search for ports maintained by this maintainer
Port Added: 10 Jul 2000 01:17:41
crimap 2.4 search for ports that depend on this port
Creation of multilocus linkage maps

There is no maintainer for this port.
Any concerns regarding this port should be directed to the FreeBSD Ports mailing list via ports@FreeBSD.org search for ports maintained by this maintainer
Port Added: 27 Mar 2002 14:43:13
cycle 0.3.1_2* search for ports that depend on this port
A calendar program for women
Maintained by: danfe@FreeBSD.org search for ports maintained by this maintainer
Port Added: 30 Jun 2005 15:05:46
Also Listed In: deskutils python
distribfold 0.1.20040613 search for ports that depend on this port
distributedfolding.org distributed protein folding project

There is no maintainer for this port.
Any concerns regarding this port should be directed to the FreeBSD Ports mailing list via ports@FreeBSD.org search for ports maintained by this maintainer
Port Added: 07 Oct 2002 04:07:30
Also Listed In: net
dna-qc 1993.07.26 search for ports that depend on this port
A quality control algorithm for DNA sequencing projects

There is no maintainer for this port.
Any concerns regarding this port should be directed to the FreeBSD Ports mailing list via ports@FreeBSD.org search for ports maintained by this maintainer
Port Added: 19 Dec 2001 00:20:48
dotter 20021204 search for ports that depend on this port
Ignore IGNORE: is only for i386, while you are running amd64
A viewer for multiple sequence alignments
Maintained by: fernan@iib.unsam.edu.ar search for ports maintained by this maintainer
Port Added: 15 Mar 2006 10:36:50
dtiquery 1.1* search for ports that depend on this port
Ignore IGNORE: you must manually fetch dtiquery-1.1.tar.gz from http://graphics.stanford.edu/projects/dti/, place it in /usr/ports/distfiles, and then run make again
Restricted RESTRICTED: Must register to download at http://graphics.stanford.edu/projects/dti/
Stanford DTI Visualization tool
Maintained by: jwbacon@tds.net search for ports maintained by this maintainer
Port Added: 25 Feb 2008 12:56:30
Also Listed In: science
embassy 5.0.0 search for ports that depend on this port
A collection of contributed EMBOSS applications
Maintained by: fernan@iib.unsam.edu.ar search for ports maintained by this maintainer
Port Added: 26 Nov 2004 16:35:20
emboss 5.0.0 search for ports that depend on this port
A collection of open source tools for genetic sequence analysis
Maintained by: fernan@iib.unsam.edu.ar search for ports maintained by this maintainer
Port Added: 31 Jul 2000 17:13:54
fasta 21.u1.d1 search for ports that depend on this port
NO CDROM NO CDROM: May not be sold or incorporated into a commercial product
A collection of programs for searching DNA and protein databases

There is no maintainer for this port.
Any concerns regarding this port should be directed to the FreeBSD Ports mailing list via ports@FreeBSD.org search for ports maintained by this maintainer
Port Added: 11 Feb 2001 13:24:20
fasta3 35.3.6 search for ports that depend on this port
NO CDROM NO CDROM: May not be sold or incorporated into a commercial product
A collection of programs for searching DNA and protein databases
Maintained by: fernan@iib.unsam.edu.ar search for ports maintained by this maintainer
Port Added: 11 Feb 2001 13:29:00
fastdnaml 1.2.2_1 search for ports that depend on this port
Faster DNAML, makes phylogenetic trees using maximum likelihood

There is no maintainer for this port.
Any concerns regarding this port should be directed to the FreeBSD Ports mailing list via ports@FreeBSD.org search for ports maintained by this maintainer
Port Added: 12 Oct 2000 10:31:14
finchtv 1.3.1 search for ports that depend on this port
A chromatogram trace viewer
Maintained by: fernan@iib.unsam.edu.ar search for ports maintained by this maintainer
Port Added: 11 Mar 2005 21:16:55
fluctuate 1.40 search for ports that depend on this port
A program to fit population models

There is no maintainer for this port.
Any concerns regarding this port should be directed to the FreeBSD Ports mailing list via ports@FreeBSD.org search for ports maintained by this maintainer
Port Added: 06 Aug 2001 12:45:39
garlic 1.5_2 search for ports that depend on this port
Molecular viewer, editor and visualization program
Maintained by: maho@FreeBSD.org search for ports maintained by this maintainer
Port Added: 28 Jul 2003 07:41:18
genpak 0.26_4 search for ports that depend on this port
A set of small utilities to manipulate DNA sequences

There is no maintainer for this port.
Any concerns regarding this port should be directed to the FreeBSD Ports mailing list via ports@FreeBSD.org search for ports maintained by this maintainer
Port Added: 27 Feb 2001 23:46:53
gff2ps 0.98d_1 search for ports that depend on this port
Converts gff-formated genomic data-sets to PostScript

There is no maintainer for this port.
Any concerns regarding this port should be directed to the FreeBSD Ports mailing list via ports@FreeBSD.org search for ports maintained by this maintainer
Port Added: 19 Dec 2001 07:03:28
gmap 2006.04.21 search for ports that depend on this port
A Genomic Mapping and Alignment Program for mRNA and EST Sequences
Maintained by: rpz@cse.wustl.edu search for ports maintained by this maintainer
Port Added: 29 Sep 2006 05:09:50
gperiodic 2.0.10_1 search for ports that depend on this port
Displays a periodic table of the elements

There is no maintainer for this port.
Any concerns regarding this port should be directed to the FreeBSD Ports mailing list via ports@FreeBSD.org search for ports maintained by this maintainer
Port Added: unknown
grappa 2.0 search for ports that depend on this port
Genome Rearrangements Analysis and Phylogeny Software

There is no maintainer for this port.
Any concerns regarding this port should be directed to the FreeBSD Ports mailing list via ports@FreeBSD.org search for ports maintained by this maintainer
Port Added: 04 Jul 2001 06:39:40
hmmer 2.3.2 search for ports that depend on this port
Profile hidden Markov models for biological sequence analysis
Maintained by: fernan@iib.unsam.edu.ar search for ports maintained by this maintainer
Port Added: unknown
jalview 2.07_1 search for ports that depend on this port
A viewer and editor for multiple sequence alignments
Maintained by: fernan@iib.unsam.edu.ar search for ports maintained by this maintainer
Port Added: 13 Feb 2006 09:43:01
Also Listed In: java
kinemage 5.79_1 search for ports that depend on this port
A molecular visualization program with special functions

There is no maintainer for this port.
Any concerns regarding this port should be directed to the FreeBSD Ports mailing list via ports@FreeBSD.org search for ports maintained by this maintainer
Port Added: unknown
lagan 1.2 search for ports that depend on this port
Efficient tools for large-scale multiple alignments of genomic DNA
Maintained by: fernan@iib.unsam.edu.ar search for ports maintained by this maintainer
Port Added: 16 Mar 2006 22:31:50
lamarc 2.1.2b,1 search for ports that depend on this port
A package of programs for computing population parameters

There is no maintainer for this port.
Any concerns regarding this port should be directed to the FreeBSD Ports mailing list via ports@FreeBSD.org search for ports maintained by this maintainer
Port Added: 07 Aug 2001 06:17:58
libgenome 0.5.2_1 search for ports that depend on this port
Toolkit for developing bioinformatic related software in C++

There is no maintainer for this port.
Any concerns regarding this port should be directed to the FreeBSD Ports mailing list via ports@FreeBSD.org search for ports maintained by this maintainer
Port Added: 30 Jul 2002 11:57:35
linux-foldingathome 5.04 search for ports that depend on this port
Distributed client for Protein Folding
Maintained by: onatan@gmail.com search for ports maintained by this maintainer
Port Added: 28 Aug 2006 23:34:01
lsysexp 0.67_7 search for ports that depend on this port
A GTK based program for viewing and creating L-system fractals
Maintained by: dyeske@gmail.com search for ports maintained by this maintainer
Port Added: 03 Sep 2003 03:23:56
mafft 5.743 search for ports that depend on this port
Multiple sequence alignments based on fast Fourier transform
Maintained by: fernan@iib.unsam.edu.ar search for ports maintained by this maintainer
Port Added: 15 Mar 2006 10:41:45
mapm3 3.0 search for ports that depend on this port
Constructs linkage maps of markers segregating in experimental crosses
Maintained by: tphilipp@potion-studios.com search for ports maintained by this maintainer
Port Added: 06 Apr 2008 05:49:23
migrate 2.4.3_1 search for ports that depend on this port
A program to estimate population sizes and migration rates

There is no maintainer for this port.
Any concerns regarding this port should be directed to the FreeBSD Ports mailing list via ports@FreeBSD.org search for ports maintained by this maintainer
Port Added: 06 Aug 2001 11:07:46
minc 1.4_2* search for ports that depend on this port
Medical Imaging NetCDF
Maintained by: bacon@smithers.neuro.mcw.edu search for ports maintained by this maintainer
Port Added: 12 Feb 2006 15:31:05
Also Listed In: science
minc2 2.0.09_1* search for ports that depend on this port
Medical Imaging NetCDF
Maintained by: bacon@smithers.neuro.mcw.edu search for ports maintained by this maintainer
Port Added: 30 Apr 2006 13:09:06
Also Listed In: science
molden 4.5_2 search for ports that depend on this port
Restricted RESTRICTED: free for academic, non profit usage; do not re-distribute source and executable.
Display molecular orbitals and electron densities in 2D and 3D

There is no maintainer for this port.
Any concerns regarding this port should be directed to the FreeBSD Ports mailing list via ports@FreeBSD.org search for ports maintained by this maintainer
Port Added: unknown
mopac 7.1.10,1 search for ports that depend on this port
Semi-empirical (MNDO, etc.) molecular orbital calculation

There is no maintainer for this port.
Any concerns regarding this port should be directed to the FreeBSD Ports mailing list via ports@FreeBSD.org search for ports maintained by this maintainer
Port Added: unknown
mrbayes 3.1.2 search for ports that depend on this port
Bayesian inference of phylogeny
Maintained by: mzaki@m.u-tokyo.ac.jp search for ports maintained by this maintainer
Port Added: 15 Dec 2007 15:13:49
mummer 3.20 search for ports that depend on this port
A modular system for rapid whole genome alignment
Maintained by: Anthony.Maher@uts.edu.au search for ports maintained by this maintainer
Port Added: 14 Dec 2007 20:56:11
muscle 3.6 search for ports that depend on this port
MUltiple Sequence Comparison by Log-Expectation
Maintained by: mzaki@m.u-tokyo.ac.jp search for ports maintained by this maintainer
Port Added: 14 May 2008 14:52:50
nab 5.1.2_1 search for ports that depend on this port
Deprecated DEPRECATED: superseded by AmberTools (by same development group)
A language for macromolecules
Maintained by: mldodson@comcast.net search for ports maintained by this maintainer
Port Added: 10 Oct 2000 00:57:23
ncbi-toolkit 2006.05.07_1 search for ports that depend on this port
NCBI development toolkit, including BLAST 2 and GenBank/Entrez support
Maintained by: fernan@iib.unsam.edu.ar search for ports maintained by this maintainer
Port Added: 29 Oct 2000 10:56:24
njplot 2.1 search for ports that depend on this port
Phylogenetic tree drawing program capable of interactive manipulation
Maintained by: mzaki@m.u-tokyo.ac.jp search for ports maintained by this maintainer
Port Added: 14 May 2008 15:07:25
ortep3 1.0.3_3 search for ports that depend on this port
The Oak Ridge Thermal Ellipsoid Plot Program for Crystal Structure

There is no maintainer for this port.
Any concerns regarding this port should be directed to the FreeBSD Ports mailing list via ports@FreeBSD.org search for ports maintained by this maintainer
Port Added: unknown
p5-AcePerl 1.91 search for ports that depend on this port
Perl5 interface to the ACEDB genome database system
Maintained by: pgollucci@p6m7g8.com search for ports maintained by this maintainer
Port Added: 28 Jul 2000 11:16:10
Also Listed In: databases perl5
p5-Bio-ASN1-EntrezGene 1.091 search for ports that depend on this port
Regular expression-based Perl Parser for NCBI Entrez Gene
Maintained by: mauricio@arareko.net search for ports maintained by this maintainer
Port Added: 15 Oct 2005 21:11:03
Also Listed In: perl5
p5-Bio-Das 1.07 search for ports that depend on this port
Client-side library for Distributed Genome Annotation System
Maintained by: perl@FreeBSD.org search for ports maintained by this maintainer
Port Added: 01 Sep 2005 14:10:39
p5-Bio-Phylo 0.16 search for ports that depend on this port
Phylogenetic analysis using perl

There is no maintainer for this port.
Any concerns regarding this port should be directed to the FreeBSD Ports mailing list via ports@FreeBSD.org search for ports maintained by this maintainer
Port Added: 13 May 2006 17:50:16
Also Listed In: perl5
p5-bioperl 1.4_1 search for ports that depend on this port
A collection of Perl modules for bioinformatics
Maintained by: fernan@iib.unsam.edu.ar search for ports maintained by this maintainer
Port Added: 28 Jul 2000 12:06:03
Also Listed In: perl5
p5-bioperl-devel 1.5.1_1 search for ports that depend on this port
A collection of Perl modules for bioinformatics (developer release)
Maintained by: mauricio@arareko.net search for ports maintained by this maintainer
Port Added: 14 Aug 2001 07:36:36
Also Listed In: perl5
p5-bioperl-run 1.4_1 search for ports that depend on this port
Wrapper modules for common bioinformatics tools
Maintained by: mauricio@arareko.net search for ports maintained by this maintainer
Port Added: 02 May 2006 22:32:38
Also Listed In: perl5
p5-bioperl-run-devel 1.5.1_1 search for ports that depend on this port
Wrapper modules for common bioinformatics tools (developer release)
Maintained by: mauricio@arareko.net search for ports maintained by this maintainer
Port Added: 02 May 2006 22:34:04
Also Listed In: perl5
paml 3.15 search for ports that depend on this port
Phylogenetic Analysis by Maximum Likelihood (PAML)

There is no maintainer for this port.
Any concerns regarding this port should be directed to the FreeBSD Ports mailing list via ports@FreeBSD.org search for ports maintained by this maintainer
Port Added: 10 Jul 2000 01:21:06
phylip 3.66_2,1 search for ports that depend on this port
A Phylogeny Inference Package

There is no maintainer for this port.
Any concerns regarding this port should be directed to the FreeBSD Ports mailing list via ports@FreeBSD.org search for ports maintained by this maintainer
Port Added: 10 Jul 2000 01:25:48
platon 2007.01.09_2 search for ports that depend on this port
Restricted RESTRICTED: free for academic, US5000 for commercial users
Tool for viewing molecular/crystallographic structures

There is no maintainer for this port.
Any concerns regarding this port should be directed to the FreeBSD Ports mailing list via ports@FreeBSD.org search for ports maintained by this maintainer
Port Added: unknown
povchem 1.0_3 search for ports that depend on this port
Simple yet powerful tool to generate POV from a PDB file

There is no maintainer for this port.
Any concerns regarding this port should be directed to the FreeBSD Ports mailing list via ports@FreeBSD.org search for ports maintained by this maintainer
Port Added: unknown
Also Listed In: graphics
primer3 1.1.3 search for ports that depend on this port
Primer3 helps to choose primers for PCR reactions
Maintained by: fernan@iib.unsam.edu.ar search for ports maintained by this maintainer
Port Added: 17 Sep 2002 16:31:31
protomol 2.0.3_2 search for ports that depend on this port
OO, component based, framework for molecular dynamics (MD) simulations
Maintained by: sangwoos@gmail.com search for ports maintained by this maintainer
Port Added: 05 May 2006 21:12:57
psi88 1.0_1 search for ports that depend on this port
Plotting wavefunctions (molecular orbitals) in 3D

There is no maintainer for this port.
Any concerns regarding this port should be directed to the FreeBSD Ports mailing list via ports@FreeBSD.org search for ports maintained by this maintainer
Port Added: unknown
py-biopython 1.43 search for ports that depend on this port
A collection of Python modules for bioinformatics
Maintained by: mauricio@arareko.net search for ports maintained by this maintainer
Port Added: 31 Jul 2000 10:12:24
Also Listed In: python
pymol 1.0r2_1 search for ports that depend on this port
Free and Open-Source molecular modeling system
Maintained by: maho@FreeBSD.org search for ports maintained by this maintainer
Port Added: 13 Aug 2002 12:53:54
Also Listed In: python
rasmol 2.7.2.1.1_2 search for ports that depend on this port
Fast Molecular Visualization Program

There is no maintainer for this port.
Any concerns regarding this port should be directed to the FreeBSD Ports mailing list via ports@FreeBSD.org search for ports maintained by this maintainer
Port Added: unknown
raster3d 2.7.d_1* search for ports that depend on this port
A set of tools for generating raster images of proteins and molecules
Maintained by: shaun@FreeBSD.org search for ports maintained by this maintainer
Port Added: 28 Apr 2006 15:21:11
Also Listed In: graphics
recombine 1.41 search for ports that depend on this port
A program to fit population models across sites

There is no maintainer for this port.
Any concerns regarding this port should be directed to the FreeBSD Ports mailing list via ports@FreeBSD.org search for ports maintained by this maintainer
Port Added: 06 Aug 2001 12:49:53
ruby-bio 1.1.0 search for ports that depend on this port
Integrated environment for Bioinformatics written in Ruby
Maintained by: mauricio@arareko.net search for ports maintained by this maintainer
Port Added: 24 Oct 2001 04:21:52
Also Listed In: ruby
seaview 2006.02.13_3 search for ports that depend on this port
Multiple DNA/protein sequence alignment editor
Maintained by: fernan@iib.unsam.edu.ar search for ports maintained by this maintainer
Port Added: unknown
seqio 1.2.2 search for ports that depend on this port
A set of C functions which can read/write biological sequence files

There is no maintainer for this port.
Any concerns regarding this port should be directed to the FreeBSD Ports mailing list via ports@FreeBSD.org search for ports maintained by this maintainer
Port Added: 22 Aug 2001 10:07:26
sim4 2003.09.21 search for ports that depend on this port
An algorithm for aligning expressed DNA with genomic sequences

There is no maintainer for this port.
Any concerns regarding this port should be directed to the FreeBSD Ports mailing list via ports@FreeBSD.org search for ports maintained by this maintainer
Port Added: 27 Jul 2000 12:33:01
tRNAscan-SE 1.23 search for ports that depend on this port
An improved tool for transfer RNA detection

There is no maintainer for this port.
Any concerns regarding this port should be directed to the FreeBSD Ports mailing list via ports@FreeBSD.org search for ports maintained by this maintainer
Port Added: 27 Mar 2002 14:19:04
t_coffee 5.68 search for ports that depend on this port
A multiple DNA or protein sequence alignment package
Maintained by: fernan@iib.unsam.edu.ar search for ports maintained by this maintainer
Port Added: 25 Jan 2002 11:58:16
tinker 4.2.20040908_2 search for ports that depend on this port
Restricted RESTRICTED: author requests no distribution except from his FTP site
A general purpose molecular modelling package

There is no maintainer for this port.
Any concerns regarding this port should be directed to the FreeBSD Ports mailing list via ports@FreeBSD.org search for ports maintained by this maintainer
Port Added: unknown
treepuzzle 5.2 search for ports that depend on this port
Maximum likelihood phylogeny reconstruction using quartets
Maintained by: jan.lentfer@web.de search for ports maintained by this maintainer
Port Added: 20 Nov 2002 09:04:07
treeviewx 0.5.1_2 search for ports that depend on this port
A phylogenetic tree viewer
Maintained by: fernan@iib.unsam.edu.ar search for ports maintained by this maintainer
Port Added: 17 Aug 2001 06:39:29
wise 2.2.0 search for ports that depend on this port
Intelligent algorithms for DNA searches

There is no maintainer for this port.
Any concerns regarding this port should be directed to the FreeBSD Ports mailing list via ports@FreeBSD.org search for ports maintained by this maintainer
Port Added: 10 Sep 2002 14:59:05
xdrawchem 1.9.9_4 search for ports that depend on this port
Chemical drawing program
Maintained by: hemi@puresimplicity.net search for ports maintained by this maintainer
Port Added: 19 Jul 2000 11:23:02
xmolwt 0.7_3 search for ports that depend on this port
Calculate formula weight and percent of each element for a given formula

There is no maintainer for this port.
Any concerns regarding this port should be directed to the FreeBSD Ports mailing list via ports@FreeBSD.org search for ports maintained by this maintainer
Port Added: unknown

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