Category listing - biology |
Software related to biology.- Number of ports in this category: 159
Ports marked with a * actually reside within another category but
have biology listed as a secondary category.
|
- InsightToolkit Insight Toolkit
4.13.0_2* 
- Maintainer: woodsb02@FreeBSD.org
 Port Added: 07 Sep 2006 03:14:06
Also Listed In: science
License: APACHE20
- MOOSE-neural-simulator Multiphysics Object Oriented Simulation Environment
3.1.2_1* 
- Maintainer: yuri@FreeBSD.org
 Port Added: 19 Dec 2017 16:04:41
Also Listed In: science
License: GPLv3
- afni Advanced Functional Neuro Imaging
2015.11.13_6* 
- Maintainer: jwb@FreeBSD.org
 Port Added: 25 Jan 2006 17:37:44
Also Listed In: science graphics
License: GPLv2
- ariadne Programs to compare protein sequences and profiles
1.3 
BROKEN: No public distfiles
IGNORE: is marked as broken: No public distfiles
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  Port Added: 22 Jun 2004 14:31:00
License: not specified in port
- artemis DNA sequence viewer and annotation tool
9_2 
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  Port Added: 22 Dec 2001 11:39:40
Also Listed In: java
License: not specified in port
- avida Auto-adaptive genetic system designed for ALife research
2.12.4 
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  Port Added: 20 Apr 2002 15:17:56
License: GPLv3
- babel Converts among various molecular file formats
1.6_4 
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  Port Added: unknown
Also Listed In: converters
License: not specified in port
- bamtools API and toolkit for handling BAM files
2.5.1 
- Maintainer: jwb@FreeBSD.org
 Port Added: 28 Mar 2018 13:26:48
License: MIT
- bcftools Tools for manipulating next-generation sequencing data
1.6 
- Maintainer: cartwright@asu.edu
 Port Added: 05 Jun 2015 21:01:24
License: GPLv3
- bedtools Toolset for genome set arithmetic such as intersect, union
2.27.1 
- Maintainer: jwb@FreeBSD.org
 Port Added: 19 Jan 2016 08:56:42
License: GPLv2
- biococoa Bioinformatics framework
2.2.2_4 
- Maintainer: theraven@FreeBSD.org
 Port Added: 30 Dec 2006 09:21:22
Also Listed In: gnustep
License: LGPL21
- blat Fast tool for local sequence similarity searches
36 
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  Port Added: 15 Mar 2006 10:29:12
License: NONE
- bowtie Ultrafast, memory-efficient short read aligner
1.1.2_5 
- Maintainer: jwb@FreeBSD.org
 Port Added: 05 Mar 2016 13:21:35
License: ART10
- bowtie2 Ultrafast, memory-efficient short read aligner
2.3.3.1 
- Maintainer: jwb@FreeBSD.org
 Port Added: 23 Mar 2016 11:22:47
License: GPLv3+
- bwa Burrows-Wheeler sequence aligner
0.7.17 
- Maintainer: jwb@FreeBSD.org
 Port Added: 25 Sep 2015 18:39:48
License: GPLv3
- canu Single molecule sequence assembler
1.6_3 
- Maintainer: jwb@FreeBSD.org
 Port Added: 22 Dec 2017 01:30:37
Also Listed In: java perl5
License: GPLv2
- cd-hit Clustering and comparing protein or nucleotide sequences
4.6.6_3 
- Maintainer: jwb@FreeBSD.org
 Port Added: 19 Sep 2015 11:17:00
License: GPLv2
- cdbfasta Fast indexing and retrieval of FASTA records from flat file databases
2010.07.22 
- Maintainer: jwb@FreeBSD.org
 Port Added: 25 Sep 2015 18:37:34
License: not specified in port
- chemeq Outputs LaTeX code for chemical reaction
1.50_2 
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  Port Added: 10 Jul 2000 00:14:19
Also Listed In: textproc
License: GPLv2
- clustalw Multiple alignment program for DNA or proteins
2.1_1 
RESTRICTED: No commercial use.
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  Port Added: 10 Jul 2000 00:17:41
License: not specified in port
- consed Graphical tool for editing Phrap assemblies
27.0 
RESTRICTED: Redistribution is not permitted in any form. You must request access permission via e-mail to get the tarball. Free for academic use. Maintainer: mzaki@m.u-tokyo.ac.jp  Port Added: 24 May 2008 07:01:28
License: not specified in port
- crux Software toolkit for phylogenetic inference
1.2.0_9 
BROKEN: No public distfiles
IGNORE: is marked as broken: No public distfiles
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  Port Added: 08 Jun 2009 23:51:06
Also Listed In: python
License: BSD2CLAUSE BSD3CLAUSE
- cycle Calendar program for women
0.3.1_10* 
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  Port Added: 30 Jun 2005 14:05:46
Also Listed In: deskutils python
License: GPLv2+
- ddocent Bash pipeline for RAD sequencing
2.2.25 
- Maintainer: jwb@FreeBSD.org
 Port Added: 20 Apr 2018 01:34:22
Also Listed In: java
License: MIT
- diamond BLAST-compatible local sequence aligner
0.9.21 
- Maintainer: jrm@FreeBSD.org
 Port Added: 06 May 2016 08:45:09
License: AGPLv3
- emboss Collection of open source tools for genetic sequence analysis
6.6.0_3 
- Maintainer: wen@FreeBSD.org
 Port Added: 31 Jul 2000 16:13:54
License: GPLv2
- fasta Collection of programs for searching DNA and protein databases
21.1.1 
NO CDROM: May not be sold or incorporated into a commercial product
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  Port Added: 11 Feb 2001 13:24:20
License: not specified in port
- fasta3 Collection of programs for searching DNA and protein databases
36.3.8 
NO CDROM: May not be sold or incorporated into a commercial product Maintainer: wendell@bsd.com.br  Port Added: 11 Feb 2001 13:29:00
License: Fasta
- fastahack Utility for indexing and sequence extraction from FASTA files
g20160702 
- Maintainer: jwb@FreeBSD.org
 Port Added: 16 Apr 2018 14:50:59
License: GPLv2
- fastdnaml Faster DNAML, makes phylogenetic trees using maximum likelihood
1.2.2_2 
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  Port Added: 12 Oct 2000 09:31:14
License: GPLv2+
- fastool Simple and quick FastQ and FastA tool for file reading and conversion
0.1.4 
- Maintainer: jwb@FreeBSD.org
 Port Added: 25 Sep 2015 18:35:23
License: BSD2CLAUSE
- fastqc Quality control tool for high throughput sequence data
0.11.5 
- Maintainer: jwb@FreeBSD.org
 Port Added: 30 Nov 2017 22:54:38
Also Listed In: java perl5
License: GPLv3
- fasttree Approximately-maximum-likelihood phylogenetic trees from alignments
2.1.10_1 
- Maintainer: jwb@FreeBSD.org
 Port Added: 25 Sep 2015 18:34:35
License: GPLv2+
- fastx-toolkit CLI tools for Short-Reads FASTA/FASTQ files preprocessing
0.0.14 
- Maintainer: jwb@FreeBSD.org
 Port Added: 25 Sep 2015 18:33:28
License: AGPLv3+
- fluctuate Program to fit population models
1.40 
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  Port Added: 06 Aug 2001 11:45:39
License: not specified in port
- freebayes Bayesian haplotype-based polymorphism discovery and genotyping
1.2.0 
- Maintainer: jwb@FreeBSD.org
 Port Added: 20 Apr 2018 00:07:39
License: MIT
- garlic Molecular viewer, editor, and visualization program
1.6_1 
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  Port Added: 28 Jul 2003 06:41:18
License: not specified in port
- gff2ps Converts gff-formated genomic data-sets to PostScript
0.98d_2 
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  Port Added: 19 Dec 2001 07:03:28
License: GPLv2+
- gmap Genomic Mapping and Alignment Program for mRNA and EST Sequences
2015.09.21 
- Maintainer: jwb@FreeBSD.org
 Port Added: 29 Sep 2006 04:09:50
License: GMAP
- gperiodic Displays a periodic table of the elements
2.0.10_8 
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  Port Added: unknown
License: GPLv2+
- grappa Genome Rearrangements Analysis and Phylogeny Software
2.0 
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  Port Added: 04 Jul 2001 05:39:40
License: GPLv2
- hmmer Profile hidden Markov models for biological sequence analysis
3.1b2 
- Maintainer: mzaki@niid.go.jp
 Port Added: unknown
License: GPLv3
- htslib C library for high-throughput sequencing data formats
1.6 
- Maintainer: cartwright@asu.edu
 Port Added: 14 Dec 2014 22:35:26
Also Listed In: devel
License: BSD3CLAUSE MIT
- iolib General purpose trace file (and Experiment File) reading interface
1.14.9 
- Maintainer: danilo@FreeBSD.org
 Port Added: 28 Aug 2009 23:34:46
License: BSD3CLAUSE
- iqtree Efficient phylogenomic software by maximum likelihood
1.6.3 
- Maintainer: jrm@FreeBSD.org
 Port Added: 21 Oct 2017 16:58:02
License: GPLv2
- jalview Viewer and editor for multiple sequence alignments
2.07_2 
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  Port Added: 13 Feb 2006 09:43:01
Also Listed In: java
License: not specified in port
- jellyfish Fast, memory-efficient counting of k-mers in DNA
2.2.6_2 
- Maintainer: jwb@FreeBSD.org
 Port Added: 24 Mar 2016 13:53:24
License: GPLv3+
- kallisto Quantify abundances of transcripts from RNA-Seq data
0.43.1 
- Maintainer: jwb@FreeBSD.org
 Port Added: 02 Dec 2017 20:44:35
License: BSD2CLAUSE
- lagan Efficient tools for large-scale multiple alignments of genomic DNA
2.0_1 
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  Port Added: 16 Mar 2006 22:31:50
License: GPLv2
- lamarc Package of programs for computing population parameters
2.1.8_1,1 
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  Port Added: 07 Aug 2001 05:17:58
License: APACHE20
- libgtextutils Gordon's text utilities
0.7 
- Maintainer: jwb@FreeBSD.org
 Port Added: 25 Sep 2015 18:31:38
License: AGPLv3
- libsbml API Library for Working with SBML File
5.16.0 
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  Port Added: 28 May 2009 23:36:42
Also Listed In: devel
License: LGPL21
- linux-foldingathome Distributed client for Protein Folding
5.04 
- Maintainer: onatan@gmail.com
 Port Added: 28 Aug 2006 22:34:01
License: not specified in port
- mafft Multiple alignment program for amino acid or nucleotide sequences
7.266 
- Maintainer: cartwright@asu.edu
 Port Added: 15 Mar 2006 10:41:45
License: BSD2CLAUSE
- mapm3 Constructs linkage maps of markers segregating in experimental crosses
3.0 
- Maintainer: tphilipp@potion-studios.com
 Port Added: 06 Apr 2008 04:49:23
License: not specified in port
- migrate Program to estimate population sizes and migration rates
3.6.11 
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  Port Added: 06 Aug 2001 10:07:46
License: not specified in port
- minc2 Medical Imaging NetCDF
2.2.00_6,1* 
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  Port Added: 30 Apr 2006 12:09:06
Also Listed In: science
License: MIT
- molden Display molecular orbitals and electron densities in 2D and 3D
5.7_14,1 
RESTRICTED: free for academic, non profit usage; do not re-distribute source and executable. Maintainer: jmd@FreeBSD.org  Port Added: unknown
License: Molden
- mopac Semi-empirical (MNDO, etc.) molecular orbital calculation
7.1.15_4,1 
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  Port Added: unknown
License: GPLv2+
- mrbayes Bayesian inference of phylogeny
3.1.2_2 
- Maintainer: mzaki@m.u-tokyo.ac.jp
 Port Added: 15 Dec 2007 15:13:49
License: not specified in port
- mummer Modular system for rapid whole genome alignment
3.23_2 
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  Port Added: 14 Dec 2007 20:56:11
License: ART10
- muscle MUltiple Sequence Comparison by Log-Expectation
3.8.31 
- Maintainer: mzaki@m.u-tokyo.ac.jp
 Port Added: 14 May 2008 13:52:50
License: not specified in port
- ncbi-blast+ NCBI implementation of Basic Local Alignment Search Tool
2.7.1 
- Maintainer: jwb@FreeBSD.org
 Port Added: 30 Dec 2014 20:03:26
Also Listed In: perl5 python
License: PD
- ncbi-toolkit NCBI development toolkit, including BLAST 2 and GenBank/Entrez support
2012.06.20_1 
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  Port Added: 29 Oct 2000 10:56:24
License: not specified in port
- njplot Phylogenetic tree drawing program
2.4 
- Maintainer: jrm@FreeBSD.org
 Port Added: 14 May 2008 14:07:25
License: NONE
- p5-AcePerl Perl5 interface to the ACEDB genome database system
1.92_5 
- Maintainer: perl@FreeBSD.org
 Port Added: 28 Jul 2000 10:16:10
Also Listed In: databases perl5
License: ART10 GPLv1+
- p5-Bio-ASN1-EntrezGene Regular expression-based Perl Parser for NCBI Entrez Gene
1.72_1,1 
- Maintainer: perl@FreeBSD.org
 Port Added: 15 Oct 2005 20:11:03
Also Listed In: perl5
License: ART10 GPLv1+
- p5-Bio-Coordinate Modules for working with biological coordinates
1.007001 
- Maintainer: sunpoet@FreeBSD.org
 Port Added: 19 Dec 2016 16:00:37
Also Listed In: perl5
License: ART10 GPLv1+
- p5-Bio-Das Client-side library for Distributed Genome Annotation System
1.17_4 
- Maintainer: perl@FreeBSD.org
 Port Added: 01 Sep 2005 13:10:39
Also Listed In: perl5
License: ART10 GPLv1+
- p5-Bio-Das-Lite Perl extension for the DAS (HTTP+XML) Protocol
2.11_1 
- Maintainer: perl@FreeBSD.org
 Port Added: 01 Mar 2010 09:16:56
Also Listed In: perl5
License: ART10 GPLv1+
- p5-Bio-FeatureIO Handler for FeatureIO
1.6.905 
- Maintainer: sunpoet@FreeBSD.org
 Port Added: 15 Sep 2017 19:17:29
Also Listed In: perl5
License: ART10 GPLv1+
- p5-Bio-GFF3 Fast low-level functions for parsing and formatting GFF3
2.0_2 
- Maintainer: perl@FreeBSD.org
 Port Added: 22 Apr 2011 08:51:49
Also Listed In: perl5
License: ART10 GPLv1+
- p5-Bio-Glite Perl Interface to G-language
0.10_2 
- Maintainer: perl@FreeBSD.org
 Port Added: 02 Apr 2009 18:25:38
Also Listed In: perl5
License: not specified in port
- p5-Bio-Graphics Generate GD Images of Bio::Seq Objects
2.40_2 
- Maintainer: perl@FreeBSD.org
 Port Added: 10 Mar 2009 18:52:27
Also Listed In: perl5
License: ART10 GPLv1+
- p5-Bio-MAGETAB Data model and utility API for the MAGE-TAB format
1.31_1 
- Maintainer: perl@FreeBSD.org
 Port Added: 01 Jul 2009 09:03:56
Also Listed In: perl5
License: GPLv2
- p5-Bio-NEXUS Object-oriented Perl API for the NEXUS file format
0.78_1 
- Maintainer: perl@FreeBSD.org
 Port Added: 22 Aug 2009 20:40:26
Also Listed In: perl5
License: not specified in port
- p5-Bio-Phylo Phylogenetic analysis using Perl
2.0.1 
- Maintainer: perl@FreeBSD.org
 Port Added: 13 May 2006 16:50:16
Also Listed In: perl5
License: ART10 GPLv1+
- p5-Bio-SCF Read and Update SCF Chromatographic Sequence Files
1.03_1 
- Maintainer: wen@FreeBSD.org
 Port Added: 28 Aug 2009 23:38:55
Also Listed In: perl5
License: not specified in port
- p5-BioPerl Collection of Perl modules for bioinformatics
1.007002 
- Maintainer: perl@FreeBSD.org
 Port Added: 18 Dec 2016 15:27:08
Also Listed In: perl5
License: ART10 GPLv1+
- p5-BioPerl-Run Wrapper modules for common bioinformatics tools
1.007002 
- Maintainer: perl@FreeBSD.org
 Port Added: 18 Dec 2016 15:29:01
Also Listed In: perl5
License: ART10 GPLv1+
- p5-TrimGalore Wrapper around Cutadapt and FastQC for adapter and quality trimming
0.4.5 
- Maintainer: jwb@FreeBSD.org
 Port Added: 09 Dec 2017 13:23:40
Also Listed In: perl5
License: GPLv3
- p5-transdecoder Identify candidate coding regions within transcript sequences
2.1.0_1 
- Maintainer: jwb@FreeBSD.org
 Port Added: 16 Mar 2016 20:12:42
Also Listed In: perl5
License: BSD3CLAUSE
- paml Phylogenetic Analysis by Maximum Likelihood (PAML)
4.9c_1 
- Maintainer: jrm@FreeBSD.org
 Port Added: 10 Jul 2000 00:21:06
License: GPLv3
- pbseqan Pacific Biosciences patched and stripped down SeqAn
g20171002 
- Maintainer: jwb@FreeBSD.org
 Port Added: 21 Apr 2018 17:21:58
License: BSD3CLAUSE
- pear-merger Memory-efficient and highly accurate paired-end read merger
0.9.6 
- Maintainer: jwb@FreeBSD.org
 Port Added: 04 Apr 2018 17:21:55
License: CC-BY-NC-SA-3.0
- phrap Phrap is a program for assembling shotgun DNA sequence data
1.090518 
IGNORE: you must request the source code \(distrib.tar.gz\) via e-mail, place it manually in /var/db/repos/PORTS-head/distfiles/phrap, and then try it again
RESTRICTED: Redistribution is not permitted in any form. You must request the tarball via e-mail. Free for academic use. Maintainer: mzaki@m.u-tokyo.ac.jp  Port Added: 24 May 2008 07:03:43
License: not specified in port
- phred Base calling and quality value assignment on DNA sequencing
0.020425.c 
RESTRICTED: Redistribution is not permitted in any form. You must request the tarball via e-mail. Free for academic use. Maintainer: mzaki@m.u-tokyo.ac.jp  Port Added: 24 May 2008 07:05:09
License: not specified in port
- phylip Phylogeny Inference Package
3.697,1 
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  Port Added: 10 Jul 2000 00:25:48
License: BSD2CLAUSE
- phyml Simple, fast, and accurate algorithm to estimate large phylogenies
3.3.20180129,1 
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  Port Added: 21 Jul 2009 01:10:33
License: GPLv2
- plink Whole genome association analysis toolset
1.07_8 
BROKEN: no public distfiles
IGNORE: is marked as broken: no public distfiles Maintainer: jwb@FreeBSD.org  Port Added: 27 Sep 2012 10:00:09
Also Listed In: science
License: GPLv2
- plinkseq Toolset for working with human genetic variation data
0.10_1 
- Maintainer: jwb@FreeBSD.org
 Port Added: 27 Sep 2012 10:00:09
Also Listed In: science
License: GPLv2
- primer3 Primer3 helps to choose primers for PCR reactions
2.3.6 
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  Port Added: 17 Sep 2002 15:31:31
License: GPLv2
- protomol OO, component based, framework for molecular dynamics (MD) simulations
2.0.3_13 
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  Port Added: 05 May 2006 20:12:57
License: GPLv2
- psi88 Plotting wavefunctions (molecular orbitals) in 3D
1.0_12 
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  Port Added: unknown
License: not specified in port
- py-biom-format Biological Observation Matrix (BIOM) Format Project
2.1.6_2 
- Maintainer: jrm@FreeBSD.org
 Port Added: 09 May 2016 16:37:53
Also Listed In: python
License: BSD3CLAUSE
- py-biopython Collection of Python modules for bioinformatics
1.71 
- Maintainer: mauricio@arareko.net
 Port Added: 31 Jul 2000 09:12:24
Also Listed In: python
License: not specified in port
- py-bx-python Python module for reading, manipulating and writing genomic data sets
0.8.1_1 
- Maintainer: yuri@FreeBSD.org
 Port Added: 06 May 2017 06:28:34
Also Listed In: python
License: MIT
- py-cutadapt Finds and removes adapter sequences, primers, poly-A tails, etc
1.14 
- Maintainer: jwb@FreeBSD.org
 Port Added: 29 Nov 2017 22:17:53
Also Listed In: python
License: MIT
- py-macs2 Analysis of chromatin immunoprecipitation (ChIP) sequences
2.1.0.p20170505_1 
- Maintainer: jwb@FreeBSD.org
 Port Added: 02 Dec 2017 20:46:35
Also Listed In: python
License: BSD3CLAUSE
- py-pymol OpenGL-based molecular visualization system
2.1.0_1* 
- Maintainer: yuri@FreeBSD.org
 Port Added: 19 Dec 2017 19:49:25
Also Listed In: science python
License: PyMOL
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Latest Vulnerabilities |
13 vulnerabilities affecting 120 ports have been reported in the past 14 days
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* - modified, not new All vulnerabilities
Last updated: 2018-04-21 10:09:45
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