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We just rebooted with several updates: * new HMTLify code * no port maintainer is now highly visible (e.g. https://freshports.org/security/sssd/) * fixed search logic error when using plain/ text details at https://github.com/FreshPorts/freshports/releases/tag/2.2.34
Category listing - biology
Software related to biology. - Number of ports in this category: 254

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

InsightToolkit Insight Toolkit
5.3.0* search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
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
InsightToolkit501 Insight Toolkit
5.0.1* search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout Version 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 search for ports maintained by this maintainer
Port Added: 2022-11-16 10:45:07
Also Listed In: science
License: APACHE20
Dependency lines:
  • InsightToolkit501>0:science/InsightToolkit501
InsightToolkit521 Insight Toolkit
5.2.1* search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2022-11-19 02:06:06
Also Listed In: science
License: APACHE20
Dependency lines:
  • InsightToolkit521>0:science/InsightToolkit521
abyss Assembly By Short Sequences: parallel, paired-end sequence assembler
2.3.5_1 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2019-02-25 07:56:58
License: GPLv3
Dependency lines:
  • abyss>0:biology/abyss
ad2vcf Add allelic depth info from a SAM stream to a VCF file
0.1.6 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2021-03-23 15:15:07
License: BSD2CLAUSE
Dependency lines:
  • ad2vcf>0:biology/ad2vcf
afni Advanced Functional Neuro Imaging
23.0.02* search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
Maintainer: fernape@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2006-01-25 17:37:44
People watching this port, also watch:: exifprobe, qgis
Also Listed In: graphics perl5 python science
License: GPLv2
Dependency lines:
  • 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 View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
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 lines:
  • artemis>0:biology/artemis
atac-seq Metaport for ATAC-Seq analysis
0.1.1 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2023-01-11 23:48:07
Also Listed In: python
License: NA
Dependency lines:
  • atac-seq>0:biology/atac-seq
augustus Genome annotation tool
3.5.0_1 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2022-11-25 23:57:41
Also Listed In: science
License: GPLv3
Dependency lines:
  • augustus-gene-prediction>0:biology/augustus
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 View this port on Repology. pkg-fallout Version 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 search for ports maintained by this maintainer
Port Added: 2002-04-20 15:17:56
License: GPLv3
Dependency lines:
  • 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 View this port on Repology. pkg-fallout Version 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 search for ports maintained by this maintainer
Port Added: unknown
Also Listed In: converters
License: not specified in port
Dependency lines:
  • babel>0:biology/babel
bamtools API and toolkit for handling BAM files
2.5.2_1 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2018-03-28 13:26:48
License: MIT
Dependency lines:
  • bamtools>0:biology/bamtools
bamutil Utilities for working with SAM/BAM files
1.0.15 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2021-10-12 16:45:03
License: GPLv3
Dependency lines:
  • bamutil>0:biology/bamutil
barrnap BAsic Rapid Ribosomal RNA Predictor
0.9 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2022-11-25 03:09:22
Also Listed In: science
License: GPLv3
Dependency lines:
  • barrnap>0:biology/barrnap
bbmap BBMap short read aligner, and other bioinformatic tools
38.92 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2021-04-18 16:24:08
Also Listed In: java
License: BSD3CLAUSE
Dependency lines:
  • bbmap>0:biology/bbmap
bcftools Tools for manipulating next-generation sequencing data
1.16 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2015-06-05 21:01:24
License: MIT GPLv3
Dependency lines:
  • bcftools>0:biology/bcftools
bedtools Toolset for genome set arithmetic such as intersect, union
2.30.0 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2016-01-19 08:56:42
License: MIT
Dependency lines:
  • bedtools>0:biology/bedtools
bfc Correct sequencing errors from Illumina sequencing data
g20150417 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2021-08-23 17:30:17
License: MIT
Dependency lines:
  • bfc>0:biology/bfc
bio-mocha Bcftools plugin for mosaic chromosomal alteration analysis
1.16 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2021-12-03 13:45:06
License: MIT
Dependency lines:
  • bio-mocha>0:biology/bio-mocha
bioawk BWK awk modified for biological data
1.0.7 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2020-06-05 02:45:39
License: BSD3CLAUSE
Dependency lines:
  • bioawk>0:biology/bioawk
biococoa Bioinformatics framework
2.2.2_7 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout Version 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 search for ports maintained by this maintainer
Port Added: 2006-12-30 09:21:22
Also Listed In: gnustep
License: LGPL21
Dependency lines:
  • biococoa>0:biology/biococoa
biolibc Low-level high-performance bioinformatics library
0.2.4 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2021-03-21 15:10:53
License: BSD2CLAUSE
Dependency lines:
  • biolibc>0:biology/biolibc
biolibc-tools High-performance bioinformatics tools based on biolibc
0.1.4.1 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2021-08-30 13:12:06
License: BSD2CLAUSE
Dependency lines:
  • biolibc-tools>0:biology/biolibc-tools
bioparser C++ header-only parsing library for several formats in bioinformatics
3.0.15 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2021-01-19 07:56:57
Also Listed In: devel
License: MIT
Dependency lines:
  • bioparser>0:biology/bioparser
biosig Library for reading and writing different biosignal data format
2.5.0_1 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2021-08-17 02:54:05
License: GPLv3
Dependency lines:
  • biosig>0:biology/biosig
biosoup Collection of C++ header-only data structures for bioinformatics
0.10.0.2 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2021-01-19 09:02:17
Also Listed In: devel
License: MIT
Dependency lines:
  • biosoup>0:biology/biosoup
biostar-tools Meta-port for Biostar Handbook tools
1.10.1 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2021-06-18 22:00:16
Also Listed In: python
License: NA
Dependency lines:
  • biostar-tools>0:biology/biostar-tools
bolt-lmm Mixed model association testing and variance component analysis
2.3.6_3 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2019-05-26 03:37:05
License: GPLv3
Dependency lines:
  • bolt-lmm>0:biology/bolt-lmm
bowtie Ultrafast, memory-efficient short read aligner
1.3.1 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2016-03-05 13:21:35
License: ART10
Dependency lines:
  • bowtie>0:biology/bowtie
bowtie2 Ultrafast, memory-efficient short read aligner
2.5.1 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2016-03-23 11:22:47
Also Listed In: perl5 python
License: GPLv3+
Dependency lines:
  • bowtie2>0:biology/bowtie2
bwa Burrows-Wheeler sequence aligner
0.7.17_1 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2015-09-25 18:39:48
License: GPLv3
Dependency lines:
  • bwa>0:biology/bwa
canu Single molecule sequence assembler
2.2_2 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
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 lines:
  • canu>0:biology/canu
cd-hit Clustering and comparing protein or nucleotide sequences
4.8.1_2 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2015-09-19 11:17:00
License: GPLv2
Dependency lines:
  • 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 View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
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 lines:
  • cdbfasta>0:biology/cdbfasta
checkm Quality assessment tool for the microbial genomes
1.2.0 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
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 lines:
  • CheckM>0:biology/checkm
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 View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2018-05-21 22:15:40
License: GPLv2
Dependency lines:
  • 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 View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2000-07-10 00:17:41
License: LGPL3
Dependency lines:
  • clustalw>0:biology/clustalw
cufflinks Cufflinks assembles transcripts, estimates their abundance, etc
2.2.1.89_4 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2019-05-25 22:28:39
License: BSL
Dependency lines:
  • cufflinks>0:biology/cufflinks
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 View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2018-07-03 08:43:08
People watching this port, also watch:: recoll, chromium, firefox
Also Listed In: java
License: LGPL21
Dependency lines:
  • cytoscape>0:biology/cytoscape
ddocent Bash pipeline for RAD sequencing
2.7.8_1 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2018-04-20 01:34:22
Also Listed In: java perl5 python
License: MIT
Dependency lines:
  • dDocent>0:biology/ddocent
diamond BLAST-compatible local sequence aligner
2.0.15 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
Maintainer: jrm@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2016-05-06 08:45:09
License: GPLv3
Dependency lines:
  • diamond>0:biology/diamond
dsr-pdb Simple C++ PDB reader (reads the protein description format)
1.0.3_9 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2019-01-29 07:57:18
License: LGPL21
Dependency lines:
  • dsr-pdb>0:biology/dsr-pdb
edlib Fast C++ library for sequence alignment using edit distance
1.2.7 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2021-01-19 09:42:35
License: MIT
Dependency lines:
  • edlib>0:biology/edlib
emboss Collection of open source tools for genetic sequence analysis
6.6.0_6 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
Maintainer: wen@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2000-07-31 16:13:54
People watching this port, also watch:: graphviz
License: GPLv2
Dependency lines:
  • emboss>0:biology/emboss
erminej Analyses of gene sets such as gene expression profiling studies
3.2 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2021-07-09 12:30:08
Also Listed In: java
License: APACHE20
Dependency lines:
  • erminej>0:biology/erminej
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 View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
Maintainer: mzaki@niid.go.jp search for ports maintained by this maintainer
Port Added: 2018-07-13 07:02:53
License: GPLv3
Dependency lines:
  • exonerate>0:biology/exonerate
fasda Fast and simple differential analysis
0.1.2 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2022-12-14 00:00:46
License: BSD2CLAUSE
Dependency lines:
  • fasda>0:biology/fasda
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 View this port on Repology. pkg-fallout Version 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 search for ports maintained by this maintainer
Port Added: 2001-02-11 13:24:20
License: FASTA
Dependency lines:
  • 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 View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
Maintainer: wendell@bsd.com.br search for ports maintained by this maintainer
Port Added: 2001-02-11 13:29:00
License: Fasta
Dependency lines:
  • fasta3>0:biology/fasta3
fastahack Utility for indexing and sequence extraction from FASTA files
1.0.0 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2018-04-16 14:50:59
License: GPLv2
Dependency lines:
  • 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 View this port on Repology. pkg-fallout Version 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 search for ports maintained by this maintainer
Port Added: 2000-10-12 09:31:14
License: GPLv2+
Dependency lines:
  • 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 View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2015-09-25 18:35:23
License: BSD2CLAUSE
Dependency lines:
  • fastool>0:biology/fastool
fastp Ultra-fast all-in-one FASTQ preprocessor
0.23.2_1 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2019-05-03 14:42:13
License: MIT
Dependency lines:
  • fastp>0:biology/fastp
fastq-trim Lightening fast sequence read trimmer
0.1.2 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2022-03-19 12:27:08
License: BSD2CLAUSE
Dependency lines:
  • fastq-trim>0:biology/fastq-trim
fastqc Quality control tool for high throughput sequence data
0.11.9 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
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 lines:
  • fastqc>0:biology/fastqc
fasttree Approximately-maximum-likelihood phylogenetic trees from alignments
2.1.10_5 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2015-09-25 18:34:35
License: GPLv2+
Dependency lines:
  • 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 View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2015-09-25 18:33:28
License: AGPLv3+
Dependency lines:
  • fastx_toolkit>0:biology/fastx-toolkit
figtree Graphical viewer of phylogenetic trees
1.4.4.14 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2019-02-03 21:14:55
Also Listed In: education java
License: GPLv2
Dependency lines:
  • figtree>0:biology/figtree
flash Fast Length Adjustment of SHort reads
1.2.11 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2021-08-23 17:30:09
License: GPLv3
Dependency lines:
  • flash>0:biology/flash
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 View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
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 lines:
  • fluctuate>0:biology/fluctuate
freebayes Bayesian haplotype-based polymorphism discovery and genotyping
1.3.6_2 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2018-04-20 00:07:39
License: MIT
Dependency lines:
  • 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 View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
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Port Added: 2003-07-28 06:41:18
License: not specified in port
Dependency lines:
  • garlic>0:biology/garlic
gatk Variant discovery in high-throughput sequencing data
4.3.0.0 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
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 lines:
  • gatk>0:biology/gatk
gcta Genome-wide Complex Trait Analysis
1.26.0_3 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2020-04-15 15:22:11
License: GPLv3
Dependency lines:
  • gcta>0:biology/gcta
gemma Genome-wide Efficient Mixed Model Association
0.98.3_2 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2019-05-17 14:45:38
License: GPLv3
Dependency lines:
  • gemma>0:biology/gemma
generand Generate random genomic data in FASTA/FASTQ, SAM, or VCF format
0.1.2 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2021-03-15 20:10:03
License: BSD2CLAUSE
Dependency lines:
  • generand>0:biology/generand
gff2ps Convert gff-formatted 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 View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
Maintainer: egypcio@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2001-12-19 07:03:28
License: GPLv2+
Dependency lines:
  • gff2ps>0:biology/gff2ps
gffread GFF/GTF format conversions, filtering, FASTA extraction, etc
0.12.7 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2021-11-10 20:51:06
License: MIT
Dependency lines:
  • gffread>0:biology/gffread
gmap Genomic Mapping and Alignment Program for mRNA and EST Sequences
2020.09.12 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2006-09-29 04:09:50
License: GMAP
Dependency lines:
  • gmap>0:biology/gmap
gperiodic Displays a periodic table of the elements
3.0.3 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
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Port Added: unknown
People watching this port, also watch:: mp3rename, ladspa
License: GPLv2+
Dependency lines:
  • gperiodic>0:biology/gperiodic
graphlan High-quality circular representations of taxonomic, phylogenetic trees
1.1.3_1 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2019-02-03 20:13:43
License: MIT
Dependency lines:
  • graphlan>0:biology/graphlan
groopm Metagenomic binning suite
0.3.4_3 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
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 lines:
  • GroopM>0:biology/groopm
haplohseq Identify regions of allelic imbalance
0.1.2_6 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2019-09-16 01:07:39
License: MIT
Dependency lines:
  • haplohseq>0:biology/haplohseq
hhsuite Remote protein homology detection suite
3.3.0_1 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2019-05-19 06:52:54
Also Listed In: science
License: GPLv3
Dependency lines:
  • hhsuite>0:biology/hhsuite
hisat2 Alignment program for mapping next-generation sequencing reads
2.2.1_2 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
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 lines:
  • hisat2>0:biology/hisat2
hmmer Profile hidden Markov models for biological sequence analysis
3.3.2 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
Maintainer: mzaki@e-mail.ne.jp search for ports maintained by this maintainer
Port Added: unknown
License: BSD3CLAUSE
Dependency lines:
  • hmmer>0:biology/hmmer
htslib C library for high-throughput sequencing data formats
1.16 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2014-12-14 22:35:26
Also Listed In: devel
License: BSD3CLAUSE MIT
Dependency lines:
  • htslib>0:biology/htslib
hyphy Hypothesis testing using Phylogenies
2.5.47 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
Maintainer: jrm@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2018-05-11 00:05:33
License: MIT
Dependency lines:
  • hyphy>0:biology/hyphy
igv Visualization tool for genomic datasets
2.9.4 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
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 lines:
  • igv>0:biology/igv
infernal Search sequence databases for structural RNA homologs
1.1.4 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
Maintainer: mzaki@e-mail.ne.jp search for ports maintained by this maintainer
Port Added: 2018-06-06 15:15:35
License: BSD3CLAUSE
Dependency lines:
  • 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 View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
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Port Added: 2009-08-28 23:34:46
License: BSD3CLAUSE
Dependency lines:
  • io_lib>0:biology/iolib
iqtree Efficient phylogenomic software by maximum likelihood
2.0.6_4 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
Maintainer: jrm@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2017-10-21 16:58:02
License: GPLv2
Dependency lines:
  • iqtree>0:biology/iqtree
jalview Viewer and editor for multiple sequence alignments
2.11.2.5 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2006-02-13 09:43:01
Also Listed In: java
License: GPLv3
Dependency lines:
  • jalview>0:biology/jalview
jellyfish Fast, memory-efficient counting of k-mers in DNA
2.3.0_3 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2016-03-24 13:53:24
License: BSD3CLAUSE GPLv3+
Dependency lines:
  • Jellyfish>0:biology/jellyfish
kallisto Quantify abundances of transcripts from RNA-Seq data
0.48.0_2,1 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2017-12-02 20:44:35
License: BSD2CLAUSE
Dependency lines:
  • kallisto>0:biology/kallisto
kmcp Accurate metagenomic profiling & fast large-scale genome searching
0.9.1 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2022-08-07 20:33:13
License: MIT
Dependency lines:
  • kmcp>0:biology/kmcp
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 View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
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Port Added: 2001-08-07 05:17:58
License: APACHE20
Dependency lines:
  • lamarc>0:biology/lamarc
libbigwig C library for handling bigWig files (containing genomic data)
0.4.6 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2019-07-11 17:05:39
License: MIT
Dependency lines:
  • libbigwig>0:biology/libbigwig
libcombine C++ library for working with the COMBINE archive format
0.2.20 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2022-10-21 07:06:09
License: BSD2CLAUSE
Dependency lines:
  • libcombine>0:biology/libcombine
libgff GFF/GTF parsing library based on GCLib
2.0.0 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2021-12-05 20:51:11
License: BSL
Dependency lines:
  • libgff>0:biology/libgff
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 View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2015-09-25 18:31:38
License: AGPLv3
Dependency lines:
  • libgtextutils>0:biology/libgtextutils
libneurosim Common interfaces for neuronal simulators
1.2.0 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2021-10-08 17:21:18
License: GPLv3
Dependency lines:
  • libneurosim>0:biology/libneurosim
libnuml C++ library for Numerical Markup Language
1.1.6 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2021-09-19 06:51:03
Also Listed In: devel
License: LGPL21
Dependency lines:
  • libnuml>0:biology/libnuml
libsbml API Library for Working with SBML File
5.19.0_2 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
Maintainer: sunpoet@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2009-05-28 23:36:42
Also Listed In: devel
License: LGPL21
Dependency lines:
  • libsbml>0:biology/libsbml
libsedml C++ SED-ML library
2.0.32 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2021-09-19 18:18:23
Also Listed In: devel
License: BSD2CLAUSE
Dependency lines:
  • libsedml>0:biology/libsedml
linux-foldingathome Folding@home Client
7.6.21 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
Maintainer: 0mp@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2006-08-28 22:34:01
People watching this port, also watch:: p5-Gtk2, python
Also Listed In: linux
License: FAHSL
Dependency lines:
  • linux-foldingathome>0:biology/linux-foldingathome
mafft Multiple alignment program for amino acid or nucleotide sequences
7.267 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
Maintainer: cartwright@asu.edu search for ports maintained by this maintainer
Port Added: 2006-03-15 10:41:45
License: BSD2CLAUSE
Dependency lines:
  • mafft>0:biology/mafft
mapm3 Constructs linkage maps of markers segregating in experimental crosses
3.0_1 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
Maintainer: tphilipp@potion-studios.com search for ports maintained by this maintainer
Port Added: 2008-04-06 04:49:23
License: MAPMAKER
Dependency lines:
  • mapm3>0:biology/mapm3
megahit Ultra-fast single-node large and complex metagenomics assembly
1.2.9_1 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2022-11-22 16:42:09
License: GPLv3
Dependency lines:
  • megahit>0:biology/megahit
metaeuk Gene discovery and annotation for large-scale eukaryotic metagenomics
6_1 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2022-11-26 11:18:05
License: GPLv3
Dependency lines:
  • metaeuk>0:biology/metaeuk