| Category listing - biology |
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Software related to biology.
- Number of ports in this category: 188
Ports marked with a * actually reside within another category but
have biology listed as a secondary category. |
- InsightToolkit Insight Toolkit
- 5.0.1_6*
    5.0.1_5Version of this port present on the latest quarterly branch.- Maintainer: woodsb02@FreeBSD.org
- Port Added: 2006-09-07 03:14:06
People watching this port, also watch: gitg, quassel-core, emby-server, tmux - Also Listed In: science
- License: APACHE20
- Dependency lines:
-
- InsightToolkit>0:science/InsightToolkit
- abyss Assembly By Short Sequences: parallel, paired-end sequence assembler
- 2.2.4_1 2.2.4Version of this port present on the latest quarterly branch.
- Maintainer: yuri@FreeBSD.org
- Port Added: 2019-02-25 07:56:58
- License: GPLv3
- Dependency lines:
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- afni Advanced Functional Neuro Imaging
- 20.2.08* 20.1.17Version of this port present on the latest quarterly branch.
- 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: 2006-01-25 17:37:44
People watching this port, also watch: exifprobe, l0phtcrack, qgis - Also Listed In: science graphics perl5 python
- License: GPLv2
- Dependency lines:
-
- ${PYTHON_PKGNAMEPREFIX}>0:science/afni
- artemis DNA sequence viewer and annotation tool
- 17.0.1.11 17.0.1.11Version of this port present on the latest quarterly branch.
- Maintainer: yuri@FreeBSD.org
- Port Added: 2001-12-22 11:39:40
- Also Listed In: java
- License: GPLv3
- Dependency lines:
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- artemis>0:biology/artemis
- avida Auto-adaptive genetic system designed for ALife research
- 2.12.4 2.12.4Version of this port present on the latest quarterly branch.
- 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: 2002-04-20 15:17:56
- License: GPLv3
- Dependency lines:
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- babel Converts among various molecular file formats
- 1.6_4 1.6_4Version of this port present on the latest quarterly branch.
- 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
- Dependency lines:
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- bamtools API and toolkit for handling BAM files
- 2.5.1_2 2.5.1_1Version of this port present on the latest quarterly branch.
- Maintainer: jwb@FreeBSD.org
- Port Added: 2018-03-28 13:26:48
- License: MIT
- Dependency lines:
-
- bamtools>0:biology/bamtools
- bcftools Tools for manipulating next-generation sequencing data
- 1.10.2 1.9_1Version of this port present on the latest quarterly branch.
- Maintainer: jwb@FreeBSD.org
- Port Added: 2015-06-05 21:01:24
- License: MIT GPLv3
- Dependency lines:
-
- ${PYTHON_PKGNAMEPREFIX}>0:biology/bcftools
- bedtools Toolset for genome set arithmetic such as intersect, union
- 2.29.2 2.29.2Version of this port present on the latest quarterly branch.
- Maintainer: jwb@FreeBSD.org
- Port Added: 2016-01-19 08:56:42
- License: GPLv2
- Dependency lines:
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- ${PYTHON_PKGNAMEPREFIX}>0:biology/bedtools
- bioawk BWK awk modified for biological data
- 1.0.7 1.0.7Version of this port present on the latest quarterly branch.
- Maintainer: jwb@FreeBSD.org
- Port Added: 2020-06-05 02:45:39
- License: BSD3CLAUSE
- Dependency lines:
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- biococoa Bioinformatics framework
- 2.2.2_6 2.2.2_6Version of this port present on the latest quarterly branch.
- 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: 2006-12-30 09:21:22
- Also Listed In: gnustep
- License: LGPL21
- Dependency lines:
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- biococoa>0:biology/biococoa
- bolt-lmm Mixed model association testing and variance component analysis
- 2.3.4_4 2.3.4_4Version of this port present on the latest quarterly branch.
- Maintainer: jwb@FreeBSD.org
- Port Added: 2019-05-26 03:37:05
- License: GPLv3
- Dependency lines:
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- bolt-lmm>0:biology/bolt-lmm
- bowtie Ultrafast, memory-efficient short read aligner
- 1.1.2_9 1.1.2_9Version of this port present on the latest quarterly branch.
- Maintainer: jwb@FreeBSD.org
- Port Added: 2016-03-05 13:21:35
- License: ART10
- Dependency lines:
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- ${PYTHON_PKGNAMEPREFIX}>0:biology/bowtie
- bowtie2 Ultrafast, memory-efficient short read aligner
- 2.4.1_2 2.4.1_1Version of this port present on the latest quarterly branch.
- Maintainer: jwb@FreeBSD.org
- Port Added: 2016-03-23 11:22:47
- Also Listed In: perl5 python
- License: GPLv3+
- Dependency lines:
-
- ${PYTHON_PKGNAMEPREFIX}>0:biology/bowtie2
- bwa Burrows-Wheeler sequence aligner
- 0.7.17 0.7.17Version of this port present on the latest quarterly branch.
- Maintainer: jwb@FreeBSD.org
- Port Added: 2015-09-25 18:39:48
- License: GPLv3
- Dependency lines:
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- canu Single molecule sequence assembler
- 2.0 2.0Version of this port present on the latest quarterly branch.
- Maintainer: jwb@FreeBSD.org
- Port Added: 2017-12-22 01:30:37
- Also Listed In: java perl5
- License: GPLv2
- Dependency lines:
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- cd-hit Clustering and comparing protein or nucleotide sequences
- 4.8.1_1 4.8.1_1Version of this port present on the latest quarterly branch.
- Maintainer: jwb@FreeBSD.org
- Port Added: 2015-09-19 11:17:00
- License: GPLv2
- Dependency lines:
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- cdbfasta Fast indexing and retrieval of FASTA records from flat file databases
- 2010.07.22 2010.07.22Version of this port present on the latest quarterly branch.
- Maintainer: jwb@FreeBSD.org
- Port Added: 2015-09-25 18:37:34
- License: not specified in port
- Dependency lines:
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- cdbfasta>0:biology/cdbfasta
- checkm Quality assessment tool for the microbial genomes
- 1.0.18 1.0.18Version of this port present on the latest quarterly branch.
- Maintainer: yuri@FreeBSD.org
- Port Added: 2018-12-07 00:26:14
- Also Listed In: python
- License: GPLv3
- Dependency lines:
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- ${PYTHON_PKGNAMEPREFIX}>0:biology/checkm
- clustal-omega Multiple alignment of nucleic acid and protein, replaces clustalw
- 1.2.4 1.2.4Version of this port present on the latest quarterly branch.
- Maintainer: jwb@FreeBSD.org
- Port Added: 2018-05-21 22:15:40
- License: GPLv2
- Dependency lines:
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- clustal-omega>0:biology/clustal-omega
- clustalw Multiple alignment program for DNA or proteins
- 2.1_2 2.1_2Version of this port present on the latest quarterly branch.
- Maintainer: jwb@FreeBSD.org
- Port Added: 2000-07-10 00:17:41
- License: LGPL3
- Dependency lines:
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- clustalw>0:biology/clustalw
- cufflinks Cufflinks assembles transcripts, estimates their abundance, etc
- 2.2.1.89_1 2.2.1.89Version of this port present on the latest quarterly branch.
- Maintainer: yuri@FreeBSD.org
- Port Added: 2019-05-25 22:28:39
- License: BSL
- Dependency lines:
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- ${PYTHON_PKGNAMEPREFIX}>0:biology/cufflinks
- cytoscape Software to visualize molecular interaction networks, gene expression
- 3.6.1 3.6.1Version of this port present on the latest quarterly branch.
- Maintainer: yuri@FreeBSD.org
- Port Added: 2018-07-03 08:43:08
- Also Listed In: java
- License: LGPL21
- Dependency lines:
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- cytoscape>0:biology/cytoscape
- ddocent Bash pipeline for RAD sequencing
- 2.7.8_1 2.7.8_1Version of this port present on the latest quarterly branch.
- Maintainer: jwb@FreeBSD.org
- Port Added: 2018-04-20 01:34:22
- Also Listed In: java perl5 python
- License: MIT
- Dependency lines:
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- ${PYTHON_PKGNAMEPREFIX}>0:biology/ddocent
- diamond BLAST-compatible local sequence aligner
- 2.0.0 0.9.35Version of this port present on the latest quarterly branch.
- Maintainer: jrm@FreeBSD.org
- Port Added: 2016-05-06 08:45:09
- License: GPLv3
- Dependency lines:
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- diamond>0:biology/diamond
- dsr-pdb Simple C++ PDB reader (reads the protein description format)
- 1.0.3_5 1.0.3_5Version of this port present on the latest quarterly branch.
- Maintainer: yuri@FreeBSD.org
- Port Added: 2019-01-29 07:57:18
- License: LGPL21
- Dependency lines:
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- dsr-pdb>0:biology/dsr-pdb
- emboss Collection of open source tools for genetic sequence analysis
- 6.6.0_4 6.6.0_4Version of this port present on the latest quarterly branch.
- Maintainer: wen@FreeBSD.org
- Port Added: 2000-07-31 16:13:54
People watching this port, also watch: graphviz - License: GPLv2
- Dependency lines:
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- emboss>0:biology/emboss
- libacd.so:biology/emboss
- exonerate Generic tool for sequence alignment
- 2.4.0 2.4.0Version of this port present on the latest quarterly branch.
- Maintainer: mzaki@niid.go.jp
- Port Added: 2018-07-13 07:02:53
- License: GPLv3
- Dependency lines:
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- exonerate>0:biology/exonerate
- fasta Collection of programs for searching DNA and protein databases
- 21.1.1 21.1.1Version of this port present on the latest quarterly branch.
-
 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: 2001-02-11 13:24:20
- License: not specified in port
- Dependency lines:
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- fasta3 Collection of programs for searching DNA and protein databases
- 36.3.8 36.3.8Version of this port present on the latest quarterly branch.
-
- NO CDROM: May not be sold or incorporated into a commercial product
- Maintainer: wendell@bsd.com.br
- Port Added: 2001-02-11 13:29:00
- License: Fasta
- Dependency lines:
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- fastahack Utility for indexing and sequence extraction from FASTA files
- 1.0.0 1.0.0Version of this port present on the latest quarterly branch.
- Maintainer: jwb@FreeBSD.org
- Port Added: 2018-04-16 14:50:59
- License: GPLv2
- Dependency lines:
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- fastahack>0:biology/fastahack
- fastdnaml Faster DNAML, makes phylogenetic trees using maximum likelihood
- 1.2.2_2 1.2.2_2Version of this port present on the latest quarterly branch.
- 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: 2000-10-12 09:31:14
- License: GPLv2+
- Dependency lines:
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- fastdnaml>0:biology/fastdnaml
- fastool Simple and quick FastQ and FastA tool for file reading and conversion
- 0.1.4 0.1.4Version of this port present on the latest quarterly branch.
- Maintainer: jwb@FreeBSD.org
- Port Added: 2015-09-25 18:35:23
- License: BSD2CLAUSE
- Dependency lines:
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- fastool>0:biology/fastool
- fastp Ultra-fast all-in-one FASTQ preprocessor
- 0.20.1 0.20.1Version of this port present on the latest quarterly branch.
- Maintainer: jwb@FreeBSD.org
- Port Added: 2019-05-03 14:42:13
- License: MIT
- Dependency lines:
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- fastqc Quality control tool for high throughput sequence data
- 0.11.8 0.11.8Version of this port present on the latest quarterly branch.
- Maintainer: jwb@FreeBSD.org
- Port Added: 2017-11-30 22:54:38
- Also Listed In: java perl5
- License: GPLv3
- Dependency lines:
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- fasttree Approximately-maximum-likelihood phylogenetic trees from alignments
- 2.1.10_4 2.1.10_4Version of this port present on the latest quarterly branch.
- Maintainer: jwb@FreeBSD.org
- Port Added: 2015-09-25 18:34:35
- License: GPLv2+
- Dependency lines:
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- FastTree>0:biology/fasttree
- fastx-toolkit CLI tools for Short-Reads FASTA/FASTQ files preprocessing
- 0.0.14 0.0.14Version of this port present on the latest quarterly branch.
- Maintainer: jwb@FreeBSD.org
- Port Added: 2015-09-25 18:33:28
- License: AGPLv3+
- Dependency lines:
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- fastx_toolkit>0:biology/fastx-toolkit
- figtree Graphical viewer of phylogenetic trees
- 1.4.4 1.4.4Version of this port present on the latest quarterly branch.
- Maintainer: yuri@FreeBSD.org
- Port Added: 2019-02-03 21:14:55
- Also Listed In: java
- License: GPLv2
- Dependency lines:
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- figtree>0:biology/figtree
- fluctuate Program to fit population models
- 1.40 1.40Version of this port present on the latest quarterly branch.
- 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: 2001-08-06 11:45:39
- License: not specified in port
- Dependency lines:
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- fluctuate>0:biology/fluctuate
- freebayes Bayesian haplotype-based polymorphism discovery and genotyping
- 1.2.0_2 1.2.0_2Version of this port present on the latest quarterly branch.
- Maintainer: jwb@FreeBSD.org
- Port Added: 2018-04-20 00:07:39
- License: MIT
- Dependency lines:
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- freebayes>0:biology/freebayes
- garlic Molecular viewer, editor, and visualization program
- 1.6_1 1.6_1Version of this port present on the latest quarterly branch.
- 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: 2003-07-28 06:41:18
- License: not specified in port
- Dependency lines:
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- gatk Variant discovery in high-throughput sequencing data
- 4.1.8.0 4.1.7.0Version of this port present on the latest quarterly branch.
- Maintainer: yuri@FreeBSD.org
- Port Added: 2018-12-03 08:41:01
- Also Listed In: java
- License: BSD3CLAUSE
- Dependency lines:
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- gcta Genome-wide Complex Trait Analysis
- 1.26.0_1 1.26.0_1Version of this port present on the latest quarterly branch.
- Maintainer: jwb@FreeBSD.org
- Port Added: 2020-04-15 15:22:11
- License: GPLv3
- Dependency lines:
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- gemma Genome-wide Efficient Mixed Model Association
- 0.98.1_5 0.98.1_5Version of this port present on the latest quarterly branch.
- Maintainer: jwb@FreeBSD.org
- Port Added: 2019-05-17 14:45:38
- License: GPLv3
- Dependency lines:
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- gff2ps Converts gff-formated genomic data-sets to PostScript
- 0.98l 0.98lVersion of this port present on the latest quarterly branch.
- Maintainer: egypcio@FreeBSD.org
- Port Added: 2001-12-19 07:03:28
- License: GPLv2+
- Dependency lines:
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- gmap Genomic Mapping and Alignment Program for mRNA and EST Sequences
- 2015.09.21 2015.09.21Version of this port present on the latest quarterly branch.
- Maintainer: jwb@FreeBSD.org
- Port Added: 2006-09-29 04:09:50
- License: GMAP
- Dependency lines:
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- gperiodic Displays a periodic table of the elements
- 3.0.3 3.0.3Version of this port present on the latest quarterly branch.
- 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
People watching this port, also watch: mp3rename, ladspa - License: GPLv2+
- Dependency lines:
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- gperiodic>0:biology/gperiodic
- graphlan High-quality circular representations of taxonomic, phylogenetic trees
- 1.1.3 1.1.3Version of this port present on the latest quarterly branch.
-
 DEPRECATED: Uses deprecated version of python
 EXPIRATION DATE: 2020-08-15
- Maintainer: yuri@FreeBSD.org
- Port Added: 2019-02-03 20:13:43
- License: MIT
- Dependency lines:
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- ${PYTHON_PKGNAMEPREFIX}>0:biology/graphlan
- grappa Genome Rearrangements Analysis and Phylogeny Software
- 2.0 2.0Version of this port present on the latest quarterly branch.
- 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: 2001-07-04 05:39:40
- License: GPLv2
- Dependency lines:
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- groopm Metagenomic binning suite
- 0.3.4_2 0.3.4_2Version of this port present on the latest quarterly branch.
-
- DEPRECATED: Uses deprecated version of python
EXPIRATION DATE: 2020-08-15
- Maintainer: yuri@FreeBSD.org
- Port Added: 2018-12-07 00:10:56
- Also Listed In: python
- License: GPLv3
- Dependency lines:
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- ${PYTHON_PKGNAMEPREFIX}>0:biology/groopm
- haplohseq Identify regions of allelic imbalance
- 0.1.2_2 0.1.2_2Version of this port present on the latest quarterly branch.
-
- DEPRECATED: Uses deprecated version of python
EXPIRATION DATE: 2020-09-15
- Maintainer: jwb@FreeBSD.org
- Port Added: 2019-09-16 01:07:39
- License: MIT
- Dependency lines:
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- ${PYTHON_PKGNAMEPREFIX}>0:biology/haplohseq
- hhsuite Remote protein homology detection suite
- 3.2.0_4 3.2.0_4Version of this port present on the latest quarterly branch.
- Maintainer: yuri@FreeBSD.org
- Port Added: 2019-05-19 06:52:54
- Also Listed In: science
- License: GPLv3
- Dependency lines:
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- ${PYTHON_PKGNAMEPREFIX}>0:biology/hhsuite
- hisat2 Alignment program for mapping next-generation sequencing reads
- 2.1.0.23 2.1.0.23Version of this port present on the latest quarterly branch.
- Maintainer: jwb@FreeBSD.org
- Port Added: 2019-01-11 16:02:24
- Also Listed In: perl5 python
- License: GPLv3
- Dependency lines:
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- ${PYTHON_PKGNAMEPREFIX}>0:biology/hisat2
- hmmer Profile hidden Markov models for biological sequence analysis
- 3.3 3.3Version of this port present on the latest quarterly branch.
- Maintainer: mzaki@e-mail.ne.jp
- Port Added: unknown
- License: BSD3CLAUSE
- Dependency lines:
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- ${PYTHON_PKGNAMEPREFIX}>0:biology/hmmer
- htslib C library for high-throughput sequencing data formats
- 1.10.2 1.9Version of this port present on the latest quarterly branch.
- Maintainer: jwb@FreeBSD.org
- Port Added: 2014-12-14 22:35:26
- Also Listed In: devel
- License: BSD3CLAUSE MIT
- Dependency lines:
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- htslib>0:biology/htslib
- libhts.so:biology/htslib
- hyphy Hypothesis testing using Phylogenies
- 2.5.15 2.5.15Version of this port present on the latest quarterly branch.
- Maintainer: jrm@FreeBSD.org
- Port Added: 2018-05-11 00:05:33
- License: MIT
- Dependency lines:
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- igv Visualization tool for genomic datasets
- 2.5.3 2.5.3Version of this port present on the latest quarterly branch.
-
- DEPRECATED: depends on expiring java/openjfx8-devel
EXPIRATION DATE: 2020-11-30
- Maintainer: yuri@FreeBSD.org
- Port Added: 2018-06-25 23:56:14
- Also Listed In: java
- License: MIT
- Dependency lines:
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- infernal Search sequence databases for structural RNA homologs
- 1.1.3 1.1.3Version of this port present on the latest quarterly branch.
- Maintainer: mzaki@e-mail.ne.jp
- Port Added: 2018-06-06 15:15:35
- License: BSD3CLAUSE
- Dependency lines:
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- ${PYTHON_PKGNAMEPREFIX}>0:biology/infernal
- iolib General purpose trace file (and Experiment File) reading interface
- 1.14.10 1.14.10Version of this port present on the latest quarterly branch.
- Maintainer: danilo@FreeBSD.org
- Port Added: 2009-08-28 23:34:46
- License: BSD3CLAUSE
- Dependency lines:
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- iqtree Efficient phylogenomic software by maximum likelihood
- 2.0.6 2.0.6Version of this port present on the latest quarterly branch.
- Maintainer: jrm@FreeBSD.org
- Port Added: 2017-10-21 16:58:02
- License: GPLv2
- Dependency lines:
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- jalview Viewer and editor for multiple sequence alignments
- 2.07_3 2.07_3Version of this port present on the latest quarterly branch.
- 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: 2006-02-13 09:43:01
- Also Listed In: java
- License: not specified in port
- Dependency lines:
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- jalview>0:biology/jalview
- jellyfish Fast, memory-efficient counting of k-mers in DNA
- 2.2.10_9 2.2.10_8Version of this port present on the latest quarterly branch.
- Maintainer: jwb@FreeBSD.org
- Port Added: 2016-03-24 13:53:24
- License: GPLv3+
- Dependency lines:
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- Jellyfish>0:biology/jellyfish
- kallisto Quantify abundances of transcripts from RNA-Seq data
- 0.46.1,1 0.46.2_1Version of this port present on the latest quarterly branch.
- Maintainer: jwb@FreeBSD.org
- Port Added: 2017-12-02 20:44:35
- License: BSD2CLAUSE
- Dependency lines:
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- kallisto>0:biology/kallisto
- lagan Efficient tools for large-scale multiple alignments of genomic DNA
- 2.0_1 2.0_1Version of this port present on the latest quarterly branch.
- 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: 2006-03-16 22:31:50
- License: GPLv2
- Dependency lines:
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- lamarc Package of programs for computing population parameters
- 2.1.8_1,1 2.1.8_1,1Version of this port present on the latest quarterly branch.
- 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: 2001-08-07 05:17:58
- License: APACHE20
- Dependency lines:
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- libbigwig C library for handling bigWig files (containing genomic data)
- 0.4.4 0.4.4Version of this port present on the latest quarterly branch.
- Maintainer: yuri@FreeBSD.org
- Port Added: 2019-07-11 17:05:39
- License: MIT
- Dependency lines:
-
- libbigwig>0:biology/libbigwig
- libgtextutils Gordon's text utilities
- 0.7 0.7Version of this port present on the latest quarterly branch.
- Maintainer: jwb@FreeBSD.org
- Port Added: 2015-09-25 18:31:38
- License: AGPLv3
- Dependency lines:
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- libgtextutils>0:biology/libgtextutils
- libgtextutils.so:biology/libgtextutils
- libsbml API Library for Working with SBML File
- 5.18.0 5.18.0Version of this port present on the latest quarterly branch.
- Maintainer: sunpoet@FreeBSD.org
- Port Added: 2009-05-28 23:36:42
- Also Listed In: devel
- License: LGPL21
- Dependency lines:
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- libsbml>0:biology/libsbml
- libsbml.so:biology/libsbml
- linux-foldingathome Folding@home Client
- 7.6.13 7.6.13Version of this port present on the latest quarterly branch.
- Maintainer: 0mp@FreeBSD.org
- Port Added: 2006-08-28 22:34:01
People watching this port, also watch: gnome-vfs, p5-Gtk2, libbonoboui, python - Also Listed In: linux
- License: FAHSL
- Dependency lines:
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- linux-foldingathome>0:biology/linux-foldingathome
- mafft Multiple alignment program for amino acid or nucleotide sequences
- 7.266 7.266Version of this port present on the latest quarterly branch.
- Maintainer: cartwright@asu.edu
- Port Added: 2006-03-15 10:41:45
- License: BSD2CLAUSE
- Dependency lines:
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- mapm3 Constructs linkage maps of markers segregating in experimental crosses
- 3.0 3.0Version of this port present on the latest quarterly branch.
- Maintainer: tphilipp@potion-studios.com
- Port Added: 2008-04-06 04:49:23
- License: not specified in port
- Dependency lines:
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- migrate Program to estimate population sizes and migration rates
- 3.6.11 3.6.11Version of this port present on the latest quarterly branch.
- 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: 2001-08-06 10:07:46
- License: not specified in port
- Dependency lines:
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- migrate>0:biology/migrate
- minc2 Medical Imaging NetCDF
- 2.2.00_9,1* 2.2.00_9,1Version of this port present on the latest quarterly branch.
- 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: 2006-04-30 12:09:06
- Also Listed In: science
- License: MIT
- Dependency lines:
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- minimap2 Pairwise aligner for genomic and spliced nucleotide sequences
- 2.17 2.17Version of this port present on the latest quarterly branch.
- Maintainer: jwb@FreeBSD.org
- Port Added: 2019-04-24 18:04:07
- License: MIT
- Dependency lines:
-
- minimap2>0:biology/minimap2
- mmtf-cpp C++ MMTF format API, decoder and encoder, for molecular structures
- 1.0.0_2* 1.0.0_2Version of this port present on the latest quarterly branch.
- Maintainer: yuri@FreeBSD.org
- Port Added: 2019-02-16 10:48:32
- Also Listed In: science
- License: MIT
- Dependency lines:
-
- mmtf-cpp>0:science/mmtf-cpp
- molden Display molecular orbitals and electron densities in 2D and 3D
- 5.8.2_3,1 5.8.2_3,1Version of this port present on the latest quarterly branch.
-
 RESTRICTED: free for academic, non profit usage; do not re-distribute source and executable.
- Maintainer: jmd@FreeBSD.org
- Port Added: unknown
- License: Molden
- Dependency lines:
-
- mopac Semi-empirical (MNDO, etc.) molecular orbital calculation
- 7.1.15_8,1 7.1.15_8,1Version of this port present on the latest quarterly branch.
- 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+
- Dependency lines:
-
- mothur Software for bioinformatics of the microbial ecology community
- 1.43.0 1.43.0Version of this port present on the latest quarterly branch.
- Maintainer: yuri@FreeBSD.org
- Port Added: 2019-05-20 17:59:35
- License: GPLv3
- Dependency lines:
-
- mrbayes Bayesian inference of phylogeny
- 3.2.7_2 3.2.7_2Version of this port present on the latest quarterly branch.
- Maintainer: mzaki@e-mail.ne.jp
- Port Added: 2007-12-15 15:13:49
- License: GPLv3
- Dependency lines:
-
- mrbayes>0:biology/mrbayes
- mummer Modular system for rapid whole genome alignment
- 4.0.0.b2.2_2 4.0.0.b2.2_2Version of this port present on the latest quarterly branch.
- Maintainer: yuri@FreeBSD.org
- Port Added: 2007-12-14 20:56:11
- License: ART10
- Dependency lines:
-
- muscle MUltiple Sequence Comparison by Log-Expectation
- 3.8.1551 3.8.1551Version of this port present on the latest quarterly branch.
- Maintainer: mzaki@e-mail.ne.jp
- Port Added: 2008-05-14 13:52:50
- License: PD
- Dependency lines:
-
- ncbi-blast+ NCBI implementation of Basic Local Alignment Search Tool
- 2.10.0_1 2.10.0_1Version of this port present on the latest quarterly branch.
- Maintainer: jwb@FreeBSD.org
- Port Added: 2014-12-30 20:03:26
- Also Listed In: perl5 python
- License: PD
- Dependency lines:
-
- ${PYTHON_PKGNAMEPREFIX}blast+>0:biology/ncbi-blast+
- ncbi-cxx-toolkit NCBI C++ Toolkit
- 21.0.0_2 21.0.0_2Version of this port present on the latest quarterly branch.
- Maintainer: yuri@FreeBSD.org
- Port Added: 2018-10-08 07:55:03
- Also Listed In: science devel
- License: PD
- Dependency lines:
-
- ${PYTHON_PKGNAMEPREFIX}cxx-toolkit>0:biology/ncbi-cxx-toolkit
- ncbi-toolkit NCBI development toolkit, including BLAST 2 and GenBank/Entrez support
- 2017.01.06_5 2017.01.06_5Version of this port present on the latest quarterly branch.
- Maintainer: yuri@FreeBSD.org
- Port Added: 2000-10-29 10:56:24
People watching this port, also watch: zip, pcre, desktop-file-utils, xorg-fonts-miscbitmaps, libIDL - License: not specified in port
- Dependency lines:
-
- ncbi-toolkit>0:biology/ncbi-toolkit
- nest Simulator for spiking neural network models
- 2.20.0_1* 2.20.0_1Version of this port present on the latest quarterly branch.
- Maintainer: yuri@FreeBSD.org
- Port Added: 2019-05-11 20:30:18
- Also Listed In: science
- License: GPLv2
- Dependency lines:
-
- ${PYTHON_PKGNAMEPREFIX}>0:science/nest
- ngs-sdk Tools and libraries for using data in the INSDC Sequence Read Archives
- 2.10.5 2.10.5Version of this port present on the latest quarterly branch.
- Maintainer: yuri@FreeBSD.org
- Port Added: 2018-06-10 23:58:19
- License: PD
- Dependency lines:
-
- ngs-sdk>0:biology/ngs-sdk
- p5-AcePerl Perl5 interface to the ACEDB genome database system
- 1.92_5 1.92_5Version of this port present on the latest quarterly branch.
- Maintainer: perl@FreeBSD.org
- Port Added: 2000-07-28 10:16:10
People watching this port, also watch: libao, p5-IO-Multiplex, python, p5-Time-Piece - Also Listed In: databases perl5
- License: ART10 GPLv1+
- Dependency lines:
-
- p5-AcePerl>0:biology/p5-AcePerl
- p5-Bio-ASN1-EntrezGene Regular expression-based Perl Parser for NCBI Entrez Gene
- 1.73_2,1 1.73_2,1Version of this port present on the latest quarterly branch.
- Maintainer: sunpoet@FreeBSD.org
- Port Added: 2005-10-15 20:11:03
People watching this port, also watch: p5-Syntax-Highlight-Perl-Improved, py37-biopython, p5-XML-DOM-XPath - Also Listed In: perl5
- License: ART10 GPLv1+
- Dependency lines:
-
- p5-Bio-ASN1-EntrezGene>0:biology/p5-Bio-ASN1-EntrezGene
- p5-Bio-Cluster BioPerl cluster modules
- 1.7.3_1 1.7.3_1Version of this port present on the latest quarterly branch.
- Maintainer: sunpoet@FreeBSD.org
- Port Added: 2019-02-20 20:47:05
- Also Listed In: perl5
- License: ART10 GPLv1+
- Dependency lines:
-
- p5-Bio-Cluster>0:biology/p5-Bio-Cluster
- p5-Bio-Coordinate Modules for working with biological coordinates
- 1.007001 1.007001Version of this port present on the latest quarterly branch.
- Maintainer: sunpoet@FreeBSD.org
- Port Added: 2016-12-19 16:00:37
- Also Listed In: perl5
- License: ART10 GPLv1+
- Dependency lines:
-
- p5-Bio-Coordinate>0:biology/p5-Bio-Coordinate
- p5-Bio-DB-EMBL Database object interface for EMBL entry retrieval
- 1.7.4 1.7.4Version of this port present on the latest quarterly branch.
- Maintainer: sunpoet@FreeBSD.org
- Port Added: 2019-12-08 16:52:22
- Also Listed In: perl5
- License: ART10 GPLv1+
- Dependency lines:
-
- p5-Bio-DB-EMBL>0:biology/p5-Bio-DB-EMBL
- p5-Bio-DB-NCBIHelper Collection of routines useful for queries to NCBI databases
- 1.7.6 1.7.6Version of this port present on the latest quarterly branch.
- Maintainer: sunpoet@FreeBSD.org
- Port Added: 2019-12-08 16:52:43
- Also Listed In: perl5
- License: ART10 GPLv1+
- Dependency lines:
-
- p5-Bio-DB-NCBIHelper>0:biology/p5-Bio-DB-NCBIHelper
- p5-Bio-Das Client-side library for Distributed Genome Annotation System
- 1.17_4 1.17_4Version of this port present on the latest quarterly branch.
- Maintainer: perl@FreeBSD.org
- Port Added: 2005-09-01 13:10:39
- Also Listed In: perl5
- License: ART10 GPLv1+
- Dependency lines:
-
- p5-Bio-Das>0:biology/p5-Bio-Das
- p5-Bio-Das-Lite Perl extension for the DAS (HTTP+XML) Protocol
- 2.11_1 2.11_1Version of this port present on the latest quarterly branch.
- Maintainer: perl@FreeBSD.org
- Port Added: 2010-03-01 09:16:56
- Also Listed In: perl5
- License: ART10 GPLv1+
- Dependency lines:
-
- p5-Bio-Das-Lite>0:biology/p5-Bio-Das-Lite
- p5-Bio-FeatureIO Handler for FeatureIO
- 1.6.905 1.6.905Version of this port present on the latest quarterly branch.
- Maintainer: sunpoet@FreeBSD.org
- Port Added: 2017-09-15 19:17:29
- Also Listed In: perl5
- License: ART10 GPLv1+
- Dependency lines:
-
- p5-Bio-FeatureIO>0:biology/p5-Bio-FeatureIO
- p5-Bio-GFF3 Fast low-level functions for parsing and formatting GFF3
- 2.0_2 2.0_2Version of this port present on the latest quarterly branch.
- Maintainer: perl@FreeBSD.org
- Port Added: 2011-04-22 08:51:49
- Also Listed In: perl5
- License: ART10 GPLv1+
- Dependency lines:
-
- p5-Bio-GFF3>0:biology/p5-Bio-GFF3
- p5-Bio-Glite Perl Interface to G-language
- 0.10_2 0.10_2Version of this port present on the latest quarterly branch.
- Maintainer: perl@FreeBSD.org
- Port Added: 2009-04-02 18:25:38
- Also Listed In: perl5
- License: not specified in port
- Dependency lines:
-
- p5-Bio-Glite>0:biology/p5-Bio-Glite
- p5-Bio-Graphics Generate GD Images of Bio::Seq Objects
- 2.40_2 2.40_2Version of this port present on the latest quarterly branch.
- Maintainer: perl@FreeBSD.org
- Port Added: 2009-03-10 18:52:27
People watching this port, also watch: mkvtoolnix, rubygem-twitter4r, p5-Data-Hexdumper, py36-venusian - Also Listed In: perl5
- License: ART10 GPLv1+
- Dependency lines:
-
- p5-Bio-Graphics>0:biology/p5-Bio-Graphics
- p5-Bio-MAGETAB Data model and utility API for the MAGE-TAB format
- 1.31_2 1.31_2Version of this port present on the latest quarterly branch.
- Maintainer: perl@FreeBSD.org
- Port Added: 2009-07-01 09:03:56
- Also Listed In: perl5
- License: GPLv2
- Dependency lines:
-
- p5-Bio-MAGETAB>0:biology/p5-Bio-MAGETAB
- p5-Bio-NEXUS Object-oriented Perl API for the NEXUS file format
- 0.78_1 0.78_1Version of this port present on the latest quarterly branch.
- Maintainer: perl@FreeBSD.org
- Port Added: 2009-08-22 20:40:26
- Also Listed In: perl5
- License: not specified in port
- Dependency lines:
-
- p5-Bio-NEXUS>0:biology/p5-Bio-NEXUS
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| Latest Vulnerabilities |
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16 vulnerabilities affecting 98 ports have been reported in the past 14 days
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* - modified, not new All vulnerabilities
Last updated:
2020-08-06 18:24:49
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