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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: 159

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


Result Page: 1  2  Next
InsightToolkit Insight Toolkit
4.13.0_2* search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: woodsb02@FreeBSD.org search for ports maintained by this maintainer
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* search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
Port Added: 19 Dec 2017 16:04:41
Also Listed In: science
License: GPLv3
afni Advanced Functional Neuro Imaging
2015.11.13_6* search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
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 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Broken BROKEN: No public distfiles
Ignore 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 search for ports maintained by this maintainer
Port Added: 22 Jun 2004 14:31:00
License: not specified in port
artemis DNA sequence viewer and annotation tool
9_2 search for ports that depend on this port Find issues related to this port Report an issue related to this port

There is no maintainer for this port.
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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 search for ports that depend on this port Find issues related to this port Report an issue related to this port

There is no maintainer for this port.
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Port Added: 20 Apr 2002 15:17:56
License: GPLv3
babel Converts among various molecular file formats
1.6_4 search for ports that depend on this port Find issues related to this port Report an issue related to this port

There is no maintainer for this port.
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Port Added: unknown
Also Listed In: converters
License: not specified in port
bamtools API and toolkit for handling BAM files
2.5.1 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 28 Mar 2018 13:26:48
License: MIT
bcftools Tools for manipulating next-generation sequencing data
1.6 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: cartwright@asu.edu search for ports maintained by this maintainer
Port Added: 05 Jun 2015 21:01:24
License: GPLv3
bedtools Toolset for genome set arithmetic such as intersect, union
2.27.1 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 19 Jan 2016 08:56:42
License: GPLv2
biococoa Bioinformatics framework
2.2.2_4 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: theraven@FreeBSD.org search for ports maintained by this maintainer
Port Added: 30 Dec 2006 09:21:22
Also Listed In: gnustep
License: LGPL21
blat Fast tool for local sequence similarity searches
36 search for ports that depend on this port Find issues related to this port Report an issue related to this port

There is no maintainer for this port.
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Port Added: 15 Mar 2006 10:29:12
License: NONE
bowtie Ultrafast, memory-efficient short read aligner
1.1.2_5 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 05 Mar 2016 13:21:35
License: ART10
bowtie2 Ultrafast, memory-efficient short read aligner
2.3.3.1 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 23 Mar 2016 11:22:47
License: GPLv3+
bwa Burrows-Wheeler sequence aligner
0.7.17 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 25 Sep 2015 18:39:48
License: GPLv3
canu Single molecule sequence assembler
1.6_3 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
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 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
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 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 25 Sep 2015 18:37:34
License: not specified in port
chemeq Outputs LaTeX code for chemical reaction
1.50_2 search for ports that depend on this port Find issues related to this port Report an issue related to this port

There is no maintainer for this port.
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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 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Restricted RESTRICTED: No commercial use.

There is no maintainer for this port.
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Port Added: 10 Jul 2000 00:17:41
License: not specified in port
consed Graphical tool for editing Phrap assemblies
27.0 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Restricted 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 search for ports maintained by this maintainer
Port Added: 24 May 2008 07:01:28
License: not specified in port
crux Software toolkit for phylogenetic inference
1.2.0_9 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Broken BROKEN: No public distfiles
Ignore IGNORE: is marked as broken: No public distfiles

There is no maintainer for this port.
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Port Added: 08 Jun 2009 23:51:06
Also Listed In: python
License: BSD2CLAUSE BSD3CLAUSE
cycle Calendar program for women
0.3.1_10* search for ports that depend on this port Find issues related to this port Report an issue related to this port

There is no maintainer for this port.
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Port Added: 30 Jun 2005 14:05:46
Also Listed In: deskutils python
License: GPLv2+
ddocent Bash pipeline for RAD sequencing
2.2.25 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 20 Apr 2018 01:34:22
Also Listed In: java
License: MIT
diamond BLAST-compatible local sequence aligner
0.9.21 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: jrm@FreeBSD.org search for ports maintained by this maintainer
Port Added: 06 May 2016 08:45:09
License: AGPLv3
emboss Collection of open source tools for genetic sequence analysis
6.6.0_3 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: wen@FreeBSD.org search for ports maintained by this maintainer
Port Added: 31 Jul 2000 16:13:54
License: GPLv2
fasta Collection of programs for searching DNA and protein databases
21.1.1 search for ports that depend on this port Find issues related to this port Report an issue related to this port
NO CDROM NO CDROM: May not be sold or incorporated into a commercial product

There is no maintainer for this port.
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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 search for ports that depend on this port Find issues related to this port Report an issue related to this port
NO CDROM NO CDROM: May not be sold or incorporated into a commercial product
Maintainer: wendell@bsd.com.br search for ports maintained by this maintainer
Port Added: 11 Feb 2001 13:29:00
License: Fasta
fastahack Utility for indexing and sequence extraction from FASTA files
g20160702 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 16 Apr 2018 14:50:59
License: GPLv2
fastdnaml Faster DNAML, makes phylogenetic trees using maximum likelihood
1.2.2_2 search for ports that depend on this port Find issues related to this port Report an issue related to this port

There is no maintainer for this port.
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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 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 25 Sep 2015 18:35:23
License: BSD2CLAUSE
fastqc Quality control tool for high throughput sequence data
0.11.5 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
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 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 25 Sep 2015 18:34:35
License: GPLv2+
fastx-toolkit CLI tools for Short-Reads FASTA/FASTQ files preprocessing
0.0.14 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 25 Sep 2015 18:33:28
License: AGPLv3+
fluctuate Program to fit population models
1.40 search for ports that depend on this port Find issues related to this port Report an issue related to this port

There is no maintainer for this port.
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Port Added: 06 Aug 2001 11:45:39
License: not specified in port
freebayes Bayesian haplotype-based polymorphism discovery and genotyping
1.2.0 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 20 Apr 2018 00:07:39
License: MIT
garlic Molecular viewer, editor, and visualization program
1.6_1 search for ports that depend on this port Find issues related to this port Report an issue related to this port

There is no maintainer for this port.
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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 search for ports that depend on this port Find issues related to this port Report an issue related to this port

There is no maintainer for this port.
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Port Added: 19 Dec 2001 07:03:28
License: GPLv2+
gmap Genomic Mapping and Alignment Program for mRNA and EST Sequences
2015.09.21 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 29 Sep 2006 04:09:50
License: GMAP
gperiodic Displays a periodic table of the elements
2.0.10_8 search for ports that depend on this port Find issues related to this port Report an issue related to this port

There is no maintainer for this port.
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Port Added: unknown
License: GPLv2+
grappa Genome Rearrangements Analysis and Phylogeny Software
2.0 search for ports that depend on this port Find issues related to this port Report an issue related to this port

There is no maintainer for this port.
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Port Added: 04 Jul 2001 05:39:40
License: GPLv2
hmmer Profile hidden Markov models for biological sequence analysis
3.1b2 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: mzaki@niid.go.jp search for ports maintained by this maintainer
Port Added: unknown
License: GPLv3
htslib C library for high-throughput sequencing data formats
1.6 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: cartwright@asu.edu search for ports maintained by this maintainer
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 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: danilo@FreeBSD.org search for ports maintained by this maintainer
Port Added: 28 Aug 2009 23:34:46
License: BSD3CLAUSE
iqtree Efficient phylogenomic software by maximum likelihood
1.6.3 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: jrm@FreeBSD.org search for ports maintained by this maintainer
Port Added: 21 Oct 2017 16:58:02
License: GPLv2
jalview Viewer and editor for multiple sequence alignments
2.07_2 search for ports that depend on this port Find issues related to this port Report an issue related to this port

There is no maintainer for this port.
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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 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 24 Mar 2016 13:53:24
License: GPLv3+
kallisto Quantify abundances of transcripts from RNA-Seq data
0.43.1 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 02 Dec 2017 20:44:35
License: BSD2CLAUSE
lagan Efficient tools for large-scale multiple alignments of genomic DNA
2.0_1 search for ports that depend on this port Find issues related to this port Report an issue related to this port

There is no maintainer for this port.
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Port Added: 16 Mar 2006 22:31:50
License: GPLv2
lamarc Package of programs for computing population parameters
2.1.8_1,1 search for ports that depend on this port Find issues related to this port Report an issue related to this port

There is no maintainer for this port.
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Port Added: 07 Aug 2001 05:17:58
License: APACHE20
libgtextutils Gordon's text utilities
0.7 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 25 Sep 2015 18:31:38
License: AGPLv3
libsbml API Library for Working with SBML File
5.16.0 search for ports that depend on this port Find issues related to this port Report an issue related to this port

There is no maintainer for this port.
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Port Added: 28 May 2009 23:36:42
Also Listed In: devel
License: LGPL21
linux-foldingathome Distributed client for Protein Folding
5.04 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: onatan@gmail.com search for ports maintained by this maintainer
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 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: cartwright@asu.edu search for ports maintained by this maintainer
Port Added: 15 Mar 2006 10:41:45
License: BSD2CLAUSE
mapm3 Constructs linkage maps of markers segregating in experimental crosses
3.0 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: tphilipp@potion-studios.com search for ports maintained by this maintainer
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 search for ports that depend on this port Find issues related to this port Report an issue related to this port

There is no maintainer for this port.
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Port Added: 06 Aug 2001 10:07:46
License: not specified in port
minc2 Medical Imaging NetCDF
2.2.00_6,1* search for ports that depend on this port Find issues related to this port Report an issue related to this port

There is no maintainer for this port.
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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 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Restricted RESTRICTED: free for academic, non profit usage; do not re-distribute source and executable.
Maintainer: jmd@FreeBSD.org search for ports maintained by this maintainer
Port Added: unknown
License: Molden
mopac Semi-empirical (MNDO, etc.) molecular orbital calculation
7.1.15_4,1 search for ports that depend on this port Find issues related to this port Report an issue related to this port

There is no maintainer for this port.
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Port Added: unknown
License: GPLv2+
mrbayes Bayesian inference of phylogeny
3.1.2_2 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: mzaki@m.u-tokyo.ac.jp search for ports maintained by this maintainer
Port Added: 15 Dec 2007 15:13:49
License: not specified in port
mummer Modular system for rapid whole genome alignment
3.23_2 search for ports that depend on this port Find issues related to this port Report an issue related to this port

There is no maintainer for this port.
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Port Added: 14 Dec 2007 20:56:11
License: ART10
muscle MUltiple Sequence Comparison by Log-Expectation
3.8.31 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: mzaki@m.u-tokyo.ac.jp search for ports maintained by this maintainer
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 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
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 search for ports that depend on this port Find issues related to this port Report an issue related to this port

There is no maintainer for this port.
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Port Added: 29 Oct 2000 10:56:24
License: not specified in port
njplot Phylogenetic tree drawing program
2.4 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: jrm@FreeBSD.org search for ports maintained by this maintainer
Port Added: 14 May 2008 14:07:25
License: NONE
p5-AcePerl Perl5 interface to the ACEDB genome database system
1.92_5 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: perl@FreeBSD.org search for ports maintained by this maintainer
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 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: perl@FreeBSD.org search for ports maintained by this maintainer
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 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: sunpoet@FreeBSD.org search for ports maintained by this maintainer
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 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: perl@FreeBSD.org search for ports maintained by this maintainer
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 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: perl@FreeBSD.org search for ports maintained by this maintainer
Port Added: 01 Mar 2010 09:16:56
Also Listed In: perl5
License: ART10 GPLv1+
p5-Bio-FeatureIO Handler for FeatureIO
1.6.905 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: sunpoet@FreeBSD.org search for ports maintained by this maintainer
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 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: perl@FreeBSD.org search for ports maintained by this maintainer
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 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: perl@FreeBSD.org search for ports maintained by this maintainer
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 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: perl@FreeBSD.org search for ports maintained by this maintainer
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 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: perl@FreeBSD.org search for ports maintained by this maintainer
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 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: perl@FreeBSD.org search for ports maintained by this maintainer
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 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: perl@FreeBSD.org search for ports maintained by this maintainer
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 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: wen@FreeBSD.org search for ports maintained by this maintainer
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 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: perl@FreeBSD.org search for ports maintained by this maintainer
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 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: perl@FreeBSD.org search for ports maintained by this maintainer
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 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
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 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 16 Mar 2016 20:12:42
Also Listed In: perl5
License: BSD3CLAUSE
paml Phylogenetic Analysis by Maximum Likelihood (PAML)
4.9c_1 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: jrm@FreeBSD.org search for ports maintained by this maintainer
Port Added: 10 Jul 2000 00:21:06
License: GPLv3
pbseqan Pacific Biosciences patched and stripped down SeqAn
g20171002 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 21 Apr 2018 17:21:58
License: BSD3CLAUSE
pear-merger Memory-efficient and highly accurate paired-end read merger
0.9.6 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
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 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Ignore 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 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 search for ports maintained by this maintainer
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 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Restricted 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 search for ports maintained by this maintainer
Port Added: 24 May 2008 07:05:09
License: not specified in port
phylip Phylogeny Inference Package
3.697,1 search for ports that depend on this port Find issues related to this port Report an issue related to this port

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 00:25:48
License: BSD2CLAUSE
phyml Simple, fast, and accurate algorithm to estimate large phylogenies
3.3.20180129,1 search for ports that depend on this port Find issues related to this port Report an issue related to this port

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: 21 Jul 2009 01:10:33
License: GPLv2
plink Whole genome association analysis toolset
1.07_8 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Broken BROKEN: no public distfiles
Ignore IGNORE: is marked as broken: no public distfiles
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
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 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
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 search for ports that depend on this port Find issues related to this port Report an issue related to this port

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: 17 Sep 2002 15:31:31
License: GPLv2
protomol OO, component based, framework for molecular dynamics (MD) simulations
2.0.3_13 search for ports that depend on this port Find issues related to this port Report an issue related to this port

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: 05 May 2006 20:12:57
License: GPLv2
psi88 Plotting wavefunctions (molecular orbitals) in 3D
1.0_12 search for ports that depend on this port Find issues related to this port Report an issue related to this port

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
License: not specified in port
py-biom-format Biological Observation Matrix (BIOM) Format Project
2.1.6_2 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: jrm@FreeBSD.org search for ports maintained by this maintainer
Port Added: 09 May 2016 16:37:53
Also Listed In: python
License: BSD3CLAUSE
py-biopython Collection of Python modules for bioinformatics
1.71 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: mauricio@arareko.net search for ports maintained by this maintainer
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 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
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 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
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 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
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* search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
Port Added: 19 Dec 2017 19:49:25
Also Listed In: science python
License: PyMOL

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