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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: 155

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


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InsightToolkit Insight Toolkit
4.13.0_6* 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: 2006-09-07 03:14:06
Also Listed In: science
License: APACHE20

Dependency line: InsightToolkit>0:science/InsightToolkit

MOOSE-neural-simulator Multiphysics Object Oriented Simulation Environment
3.1.2_7* search for ports that depend on this port Find issues related to this port Report an issue related to this port
Deprecated DEPRECATED: Qt4 has been EOL since december 2015
Expiration Date EXPIRATION DATE: 2019-03-15
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2017-12-19 16:04:41
Also Listed In: science
License: GPLv3

Dependency line: MOOSE-neural-simulator>0:science/MOOSE-neural-simulator

afni Advanced Functional Neuro Imaging
2015.11.13_8* 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: 2006-01-25 17:37:44
Also Listed In: science graphics
License: GPLv2

Dependency line: afni>0:science/afni

artemis DNA sequence viewer and annotation tool
17.0.1.11 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: 2001-12-22 11:39:40
Also Listed In: java
License: GPLv3

Dependency line: artemis>0:biology/artemis

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: 2002-04-20 15:17:56
License: GPLv3

Dependency line: avida>0:biology/avida

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

Dependency line: babel>0:biology/babel

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: 2018-03-28 13:26:48
License: MIT

Dependency line: bamtools>0:biology/bamtools

bcftools Tools for manipulating next-generation sequencing data
1.9 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: 2015-06-05 21:01:24
License: MIT GPLv3

Dependency line: bcftools>0:biology/bcftools

bedtools Toolset for genome set arithmetic such as intersect, union
2.27.1_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: 2016-01-19 08:56:42
License: GPLv2

Dependency line: bedtools>0:biology/bedtools

biococoa Bioinformatics framework
2.2.2_5 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: 2006-12-30 09:21:22
Also Listed In: gnustep
License: LGPL21

Dependency line: biococoa>0:biology/biococoa

bowtie Ultrafast, memory-efficient short read aligner
1.1.2_8 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: 2016-03-05 13:21:35
License: ART10

Dependency line: bowtie>0:biology/bowtie

bowtie2 Ultrafast, memory-efficient short read aligner
2.3.3.1_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: 2016-03-23 11:22:47
License: GPLv3+

Dependency line: bowtie2>0:biology/bowtie2

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: 2015-09-25 18:39:48
License: GPLv3

Dependency line: bwa>0:biology/bwa

canu Single molecule sequence assembler
1.8_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: 2017-12-22 01:30:37
Also Listed In: java perl5
License: GPLv2

Dependency line: canu>0:biology/canu

cd-hit Clustering and comparing protein or nucleotide sequences
4.6.6_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: 2015-09-19 11:17:00
License: GPLv2

Dependency line: cd-hit>0:biology/cd-hit

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: 2015-09-25 18:37:34
License: not specified in port

Dependency line: cdbfasta>0:biology/cdbfasta

checkm Quality assessment tool for the microbial genomes
1.0.12_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: 2018-12-07 00:26:14
Also Listed In: python
License: GPLv3

Dependency line: CheckM>0:biology/checkm

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: 2000-07-10 00:14:19
Also Listed In: textproc
License: GPLv2

Dependency line: chemeq>0:biology/chemeq

clustal-omega Multiple alignment of nucleic acid and protein, replaces clustalw
1.2.4 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: 2018-05-21 22:15:40
License: GPLv2

Dependency line: clustal-omega>0:biology/clustal-omega

clustalw Multiple alignment program for DNA or proteins
2.1_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: 2000-07-10 00:17:41
License: LGPL3

Dependency line: clustalw>0:biology/clustalw

clustalx Multiple alignment of nucleic acid and protein sequences with GUI
2.1 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Deprecated DEPRECATED: Qt4 has been EOL since december 2015
Expiration Date EXPIRATION DATE: 2019-03-15
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2018-05-21 20:56:34
License: LGPL3

Dependency line: clustalx>0:biology/clustalx

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: 2008-05-24 07:01:28
License: not specified in port

Dependency line: consed>0:biology/consed

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: 2005-06-30 14:05:46
Also Listed In: deskutils python
License: GPLv2+

Dependency line: cycle>0:deskutils/cycle

cytoscape Software to visualize molecular interaction networks, gene expression
3.6.1 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: 2018-07-03 08:43:08
Also Listed In: java
License: LGPL21

Dependency line: cytoscape>0:biology/cytoscape

ddocent Bash pipeline for RAD sequencing
2.2.25_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: 2018-04-20 01:34:22
Also Listed In: java
License: MIT

Dependency line: dDocent>0:biology/ddocent

diamond BLAST-compatible local sequence aligner
0.9.24 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: 2016-05-06 08:45:09
License: GPLv3

Dependency line: diamond>0:biology/diamond

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: 2000-07-31 16:13:54
License: GPLv2

Dependency line: emboss>0:biology/emboss

exonerate Generic tool for sequence alignment
2.4.0 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: 2018-07-13 07:02:53
License: GPLv3

Dependency line: exonerate>0:biology/exonerate

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: 2001-02-11 13:24:20
License: not specified in port

Dependency line: fasta>0:biology/fasta

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: 2001-02-11 13:29:00
License: Fasta

Dependency line: fasta3>0:biology/fasta3

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: 2018-04-16 14:50:59
License: GPLv2

Dependency line: fastahack>0:biology/fastahack

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: 2000-10-12 09:31:14
License: GPLv2+

Dependency line: fastdnaml>0:biology/fastdnaml

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: 2015-09-25 18:35:23
License: BSD2CLAUSE

Dependency line: fastool>0:biology/fastool

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: 2017-11-30 22:54:38
Also Listed In: java perl5
License: GPLv3

Dependency line: fastqc>0:biology/fastqc

fasttree Approximately-maximum-likelihood phylogenetic trees from alignments
2.1.10_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: 2015-09-25 18:34:35
License: GPLv2+

Dependency line: FastTree>0:biology/fasttree

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: 2015-09-25 18:33:28
License: AGPLv3+

Dependency line: fastx_toolkit>0:biology/fastx-toolkit

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: 2001-08-06 11:45:39
License: not specified in port

Dependency line: fluctuate>0:biology/fluctuate

freebayes Bayesian haplotype-based polymorphism discovery and genotyping
1.2.0_1 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2018-04-20 00:07:39
License: MIT

Dependency line: freebayes>0:biology/freebayes

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: 2003-07-28 06:41:18
License: not specified in port

Dependency line: garlic>0:biology/garlic

gatk Variant discovery in high-throughput sequencing data
4.0.11.0 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: 2018-12-03 08:41:01
Also Listed In: java
License: BSD3CLAUSE

Dependency line: gatk>0:biology/gatk

gff2ps Converts gff-formated genomic data-sets to PostScript
0.98l search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: egypcio@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2001-12-19 07:03:28
License: GPLv2+

Dependency line: gff2ps>0:biology/gff2ps

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: 2006-09-29 04:09:50
License: GMAP

Dependency line: gmap>0:biology/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+

Dependency line: gperiodic>0:biology/gperiodic

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: 2001-07-04 05:39:40
License: GPLv2

Dependency line: grappa>0:biology/grappa

groopm Metagenomic binning suite
0.3.4_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: 2018-12-07 00:10:56
Also Listed In: python
License: GPLv3

Dependency line: GroopM>0:biology/groopm

hisat2 Alignment program for mapping next-generation sequencing reads
2.1.0.23 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: 2019-01-11 16:02:24
Also Listed In: perl5 python
License: GPLv3

Dependency line: hisat2>0:biology/hisat2

hmmer Profile hidden Markov models for biological sequence analysis
3.2.1 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: BSD3CLAUSE

Dependency line: hmmer>0:biology/hmmer

htslib C library for high-throughput sequencing data formats
1.9 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: 2014-12-14 22:35:26
Also Listed In: devel
License: BSD3CLAUSE MIT

Dependency line: htslib>0:biology/htslib

hyphy Hypothesis testing using Phylogenies
2.3.14.16_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: 2018-05-11 00:05:33
License: MIT

Dependency line: hyphy>0:biology/hyphy

igv Visualization tool for genomic datasets
2.4.16 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: 2018-06-25 23:56:14
Also Listed In: java
License: MIT

Dependency line: igv>0:biology/igv

infernal Search sequence databases for structural RNA homologs
1.1.2 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: 2018-06-06 15:15:35
License: BSD3CLAUSE

Dependency line: infernal>0:biology/infernal

iolib General purpose trace file (and Experiment File) reading interface
1.14.10 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: 2009-08-28 23:34:46
License: BSD3CLAUSE

Dependency line: io_lib>0:biology/iolib

iqtree Efficient phylogenomic software by maximum likelihood
1.6.9_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: 2017-10-21 16:58:02
License: GPLv2

Dependency line: iqtree>0:biology/iqtree

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: 2006-02-13 09:43:01
Also Listed In: java
License: not specified in port

Dependency line: jalview>0:biology/jalview

jellyfish Fast, memory-efficient counting of k-mers in DNA
2.2.6_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: 2016-03-24 13:53:24
License: GPLv3+

Dependency line: jellyfish>0:biology/jellyfish

kallisto Quantify abundances of transcripts from RNA-Seq data
0.43.1_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: 2017-12-02 20:44:35
License: BSD2CLAUSE

Dependency line: kallisto>0:biology/kallisto

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

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Port Added: 2006-03-16 22:31:50
License: GPLv2

Dependency line: lagan>0:biology/lagan

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: 2001-08-07 05:17:58
License: APACHE20

Dependency line: lamarc>0:biology/lamarc

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: 2015-09-25 18:31:38
License: AGPLv3

Dependency line: libgtextutils>0:biology/libgtextutils

libsbml API Library for Working with SBML File
5.17.0 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: 2009-05-28 23:36:42
Also Listed In: devel
License: LGPL21

Dependency line: libsbml>0:biology/libsbml

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

There is no maintainer for this port.
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Port Added: 2006-08-28 22:34:01
License: not specified in port

Dependency line: linux-foldingathome>0:biology/linux-foldingathome

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: 2006-03-15 10:41:45
License: BSD2CLAUSE

Dependency line: mafft>0:biology/mafft

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: 2008-04-06 04:49:23
License: not specified in port

Dependency line: mapm3>0:biology/mapm3

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: 2001-08-06 10:07:46
License: not specified in port

Dependency line: migrate>0:biology/migrate

minc2 Medical Imaging NetCDF
2.2.00_8,1* 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: 2006-04-30 12:09:06
Also Listed In: science
License: MIT

Dependency line: minc2>0:science/minc2

mmtf C++ implementation of the MMTF API, decoder and encoder
g20180730_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: 2018-10-18 21:21:47
Also Listed In: science
License: MIT

Dependency line: mmtf>0:science/mmtf

molden Display molecular orbitals and electron densities in 2D and 3D
5.8.2_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: 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

Dependency line: molden>0:biology/molden

mopac Semi-empirical (MNDO, etc.) molecular orbital calculation
7.1.15_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: unknown
License: GPLv2+

Dependency line: mopac>0:biology/mopac

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: 2007-12-15 15:13:49
License: not specified in port

Dependency line: mrbayes>0:biology/mrbayes

mummer Modular system for rapid whole genome alignment
4.0.0.b2.2_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: 2007-12-14 20:56:11
License: ART10

Dependency line: mummer>0:biology/mummer

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: 2008-05-14 13:52:50
License: not specified in port

Dependency line: muscle>0:biology/muscle

ncbi-blast+ NCBI implementation of Basic Local Alignment Search Tool
2.8.1_1 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2014-12-30 20:03:26
Also Listed In: perl5 python
License: PD

Dependency line: ncbi-blast+>0:biology/ncbi-blast+

ncbi-cxx-toolkit NCBI C++ Toolkit
21.0.0_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: 2018-10-08 07:55:03
Also Listed In: science devel
License: PD

Dependency line: ncbi-cxx-toolkit>0:biology/ncbi-cxx-toolkit

ncbi-toolkit NCBI development toolkit, including BLAST 2 and GenBank/Entrez support
2017.01.06_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: 2000-10-29 10:56:24
License: not specified in port

Dependency line: ncbi-toolkit>0:biology/ncbi-toolkit

ngs-sdk Tools and libraries for using data in the INSDC Sequence Read Archives
2.9.3 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: 2018-06-10 23:58:19
License: PD

Dependency line: ngs-sdk>0:biology/ngs-sdk

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: 2000-07-28 10:16:10
Also Listed In: databases perl5
License: ART10 GPLv1+

Dependency line: p5-AcePerl>0:biology/p5-AcePerl

p5-Bio-ASN1-EntrezGene Regular expression-based Perl Parser for NCBI Entrez Gene
1.73,1 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: 2005-10-15 20:11:03
Also Listed In: perl5
License: ART10 GPLv1+

Dependency line: p5-Bio-ASN1-EntrezGene>0:biology/p5-Bio-ASN1-EntrezGene

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: 2016-12-19 16:00:37
Also Listed In: perl5
License: ART10 GPLv1+

Dependency line: p5-Bio-Coordinate>0:biology/p5-Bio-Coordinate

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: 2005-09-01 13:10:39
Also Listed In: perl5
License: ART10 GPLv1+

Dependency line: p5-Bio-Das>0:biology/p5-Bio-Das

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: 2010-03-01 09:16:56
Also Listed In: perl5
License: ART10 GPLv1+

Dependency line: p5-Bio-Das-Lite>0:biology/p5-Bio-Das-Lite

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: 2017-09-15 19:17:29
Also Listed In: perl5
License: ART10 GPLv1+

Dependency line: p5-Bio-FeatureIO>0:biology/p5-Bio-FeatureIO

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: 2011-04-22 08:51:49
Also Listed In: perl5
License: ART10 GPLv1+

Dependency line: p5-Bio-GFF3>0:biology/p5-Bio-GFF3

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: 2009-04-02 18:25:38
Also Listed In: perl5
License: not specified in port

Dependency line: p5-Bio-Glite>0:biology/p5-Bio-Glite

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: 2009-03-10 18:52:27
Also Listed In: perl5
License: ART10 GPLv1+

Dependency line: p5-Bio-Graphics>0:biology/p5-Bio-Graphics

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: 2009-07-01 09:03:56
Also Listed In: perl5
License: GPLv2

Dependency line: p5-Bio-MAGETAB>0:biology/p5-Bio-MAGETAB

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: 2009-08-22 20:40:26
Also Listed In: perl5
License: not specified in port

Dependency line: p5-Bio-NEXUS>0:biology/p5-Bio-NEXUS

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: 2006-05-13 16:50:16
Also Listed In: perl5
License: ART10 GPLv1+

Dependency line: p5-Bio-Phylo>0:biology/p5-Bio-Phylo

p5-Bio-SCF Read and Update SCF Chromatographic Sequence Files
1.03_2 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: 2009-08-28 23:38:55
Also Listed In: perl5
License: not specified in port

Dependency line: p5-Bio-SCF>0:biology/p5-Bio-SCF

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: 2016-12-18 15:27:08
Also Listed In: perl5
License: ART10 GPLv1+

Dependency line: p5-BioPerl>0:biology/p5-BioPerl

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: 2016-12-18 15:29:01
Also Listed In: perl5
License: ART10 GPLv1+

Dependency line: p5-BioPerl-Run>0:biology/p5-BioPerl-Run

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: 2017-12-09 13:23:40
Also Listed In: perl5
License: GPLv3

Dependency line: p5-TrimGalore>0:biology/p5-TrimGalore

p5-transdecoder Identify candidate coding regions within transcript sequences
5.4.0_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: 2016-03-16 20:12:42
Also Listed In: perl5
License: BSD3CLAUSE

Dependency line: p5-transdecoder>0:biology/p5-transdecoder

paml Phylogenetic Analysis by Maximum Likelihood (PAML)
4.9h 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: 2000-07-10 00:21:06
License: GPLv3

Dependency line: paml>0:biology/paml

pbbam PacBio BAM C++ library, with SWIG bindings
g20180416_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: 2018-04-23 16:08:32
License: BSD3CLAUSE

Dependency line: pbbam>0:biology/pbbam

pbcopper Core C++ library for Pacific Biosciences tools
g20180413_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: 2018-04-23 16:24:07
License: BSD3CLAUSE

Dependency line: pbcopper>0:biology/pbcopper

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: 2018-04-21 17:21:58
License: BSD3CLAUSE

Dependency line: pbseqan>0:biology/pbseqan

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: 2018-04-04 17:21:55
License: CC-BY-NC-SA-3.0

Dependency line: pear-merger>0:biology/pear-merger

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: 2008-05-24 07:03:43
License: not specified in port

Dependency line: phrap>0:biology/phrap

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: 2008-05-24 07:05:09
License: not specified in port

Dependency line: phred>0:biology/phred

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: 2000-07-10 00:25:48
License: BSD2CLAUSE

Dependency line: phylip>0:biology/phylip


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