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Why was the website so slow for so long?

The cause of the slowdown was a change to the ZFS dataset. In conjunction with the database server, very little caching was being done. This combination resulted in increased disk I/O as the system churned through the database. Details in the blog post which outlines the various things which changed. Many graphs.

Category listing - biology
Click to add this to your default watch list[s] Software related to biology.- Number of ports in this category: 177

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


Result Page: 1  2  Next
InsightToolkit Insight Toolkit
5.0.1_3* search for ports that depend on this port Find issues related to this port Report an issue related to this port 5.0.1Version of this port present on the latest quarterly branch.
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 lines:
  • InsightToolkit>0:science/InsightToolkit
abyss Assembly By Short Sequences: parallel, paired-end sequence assembler
2.2.3 search for ports that depend on this port Find issues related to this port Report an issue related to this port 2.1.5Version 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
afni Advanced Functional Neuro Imaging
19.1.20_4* search for ports that depend on this port Find issues related to this port Report an issue related to this port 19.1.20Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2006-01-25 17:37:44
Also Listed In: science graphics perl5 python
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 17.0.1.11Version 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
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 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
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 1.6Version 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
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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
2.5.1_1 search for ports that depend on this port Find issues related to this port Report an issue related to this port 2.5.1Version 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
bcftools Tools for manipulating next-generation sequencing data
1.9_1 search for ports that depend on this port Find issues related to this port Report an issue related to this port 1.9Version of this port present on the latest quarterly branch.
Maintainer: cartwright@asu.edu 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
2.29.2 search for ports that depend on this port Find issues related to this port Report an issue related to this port 2.29.2Version 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: GPLv2
Dependency lines:
  • bedtools>0:biology/bedtools
biococoa Bioinformatics framework
2.2.2_6 search for ports that depend on this port Find issues related to this port Report an issue related to this port 2.2.2Version of this port present on the latest quarterly branch.
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 lines:
  • biococoa>0:biology/biococoa
bolt-lmm Mixed model association testing and variance component analysis
2.3.4_3 search for ports that depend on this port Find issues related to this port Report an issue related to this port 2.3.4Version 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
1.1.2_9 search for ports that depend on this port Find issues related to this port Report an issue related to this port 1.1.2Version 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
2.3.5.1_2 search for ports that depend on this port Find issues related to this port Report an issue related to this port 2.3.5.1Version 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 search for ports that depend on this port Find issues related to this port Report an issue related to this port 0.7.17Version 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
1.9_1 search for ports that depend on this port Find issues related to this port Report an issue related to this port 1.9Version 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_1 search for ports that depend on this port Find issues related to this port Report an issue related to this port 4.8.1Version 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 2010.07.22Version 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
1.0.18 search for ports that depend on this port Find issues related to this port Report an issue related to this port 1.0.18Version 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 1.2.4Version 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 2.1Version 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
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 27.0Version of this port present on the latest quarterly branch.
Broken BROKEN: unfetchable
Ignore IGNORE: is marked as broken: unfetchable
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 lines:
  • consed>0:biology/consed
cufflinks Cufflinks assembles transcripts, estimates their abundance, etc
2.2.1.83_2 search for ports that depend on this port Find issues related to this port Report an issue related to this port 2.2.1.83Version 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 3.6.1Version 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
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 2.7.8Version 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
0.9.30 search for ports that depend on this port Find issues related to this port Report an issue related to this port 0.9.29Version 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_5 search for ports that depend on this port Find issues related to this port Report an issue related to this port 1.0.3Version 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
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 6.6.0Version 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
License: GPLv2
Dependency lines:
  • emboss>0:biology/emboss
  • libacd.so: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 2.4.0Version 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
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 21.1.1Version of this port present on the latest quarterly branch.
NO CDROM 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
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Port Added: 2001-02-11 13:24:20
License: not specified in port
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 36.3.8Version of this port present on the latest quarterly branch.
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 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 1.0.0Version 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 1.2.2Version 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
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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 0.1.4Version 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
0.20.0_1 search for ports that depend on this port Find issues related to this port Report an issue related to this port 0.20.0Version 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
fastqc Quality control tool for high throughput sequence data
0.11.8 search for ports that depend on this port Find issues related to this port Report an issue related to this port 0.11.8Version 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_4 search for ports that depend on this port Find issues related to this port Report an issue related to this port 2.1.10Version 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 0.0.14Version 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 search for ports that depend on this port Find issues related to this port Report an issue related to this port 1.4.4Version 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: java
License: GPLv2
Dependency lines:
  • figtree>0:biology/figtree
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 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
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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
1.2.0_2 search for ports that depend on this port Find issues related to this port Report an issue related to this port 1.2.0Version 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 1.6Version 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
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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
4.1.4.1_1 search for ports that depend on this port Find issues related to this port Report an issue related to this port 4.1.2.0.43Version 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
gemma Genome-wide Efficient Mixed Model Association
0.98.1_4 search for ports that depend on this port Find issues related to this port Report an issue related to this port 0.98.1Version 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
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 0.98lVersion 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
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 2015.09.21Version 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 3.0.3Version of this port present on the latest quarterly branch.
There is no maintainer for this port.
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Port Added: unknown
License: GPLv2+
Dependency lines:
  • gperiodic>0:biology/gperiodic
graphlan High-quality circular representations of taxonomic, phylogenetic trees
1.1.3 search for ports that depend on this port Find issues related to this port Report an issue related to this port 1.1.3Version 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
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 2.0Version of this port present on the latest quarterly branch.
There is no maintainer for this port.
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Port Added: 2001-07-04 05:39:40
License: GPLv2
Dependency lines:
  • grappa>0:biology/grappa
groopm Metagenomic binning suite
0.3.4_2 search for ports that depend on this port Find issues related to this port Report an issue related to this port 0.3.4Version 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_2 search for ports that depend on this port Find issues related to this port Report an issue related to this port 0.1.2Version 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
3.2.0_2 search for ports that depend on this port Find issues related to this port Report an issue related to this port 3.2.0Version 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
2.1.0.23 search for ports that depend on this port Find issues related to this port Report an issue related to this port 2.1.0.23Version 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 search for ports that depend on this port Find issues related to this port Report an issue related to this port 3.2.1Version 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
1.9 search for ports that depend on this port Find issues related to this port Report an issue related to this port 1.9Version of this port present on the latest quarterly branch.
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 lines:
  • htslib>0:biology/htslib
  • libhts.so:biology/htslib
hyphy Hypothesis testing using Phylogenies
2.5.4 search for ports that depend on this port Find issues related to this port Report an issue related to this port 2.3.14.16Version 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
2.5.3 search for ports that depend on this port Find issues related to this port Report an issue related to this port 2.5.3Version 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
1.1.3 search for ports that depend on this port Find issues related to this port Report an issue related to this port 1.1.2Version 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 1.14.10Version of this port present on the latest quarterly branch.
Maintainer: danilo@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2009-08-28 23:34:46
License: BSD3CLAUSE
Dependency lines:
  • io_lib>0:biology/iolib
iqtree Efficient phylogenomic software by maximum likelihood
1.6.12 search for ports that depend on this port Find issues related to this port Report an issue related to this port 1.6.12Version 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
2.07_3 search for ports that depend on this port Find issues related to this port Report an issue related to this port 2.07Version 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
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Port Added: 2006-02-13 09:43:01
Also Listed In: java
License: not specified in port
Dependency lines:
  • jalview>0:biology/jalview
jellyfish Fast, memory-efficient counting of k-mers in DNA
2.2.10_7 search for ports that depend on this port Find issues related to this port Report an issue related to this port 2.2.10Version 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: GPLv3+
Dependency lines:
  • Jellyfish>0:biology/jellyfish
kallisto Quantify abundances of transcripts from RNA-Seq data
0.46.2 search for ports that depend on this port Find issues related to this port Report an issue related to this port 0.46.1Version 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
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 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
search for ports maintained by this maintainer
Port Added: 2006-03-16 22:31:50
License: GPLv2
Dependency lines:
  • 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 2.1.8Version 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: 2001-08-07 05:17:58
License: APACHE20
Dependency lines:
  • lamarc>0:biology/lamarc
libbigwig C library for handling bigWig files (containing genomic data)
0.4.4 search for ports that depend on this port Find issues related to this port Report an issue related to this port 0.4.4Version 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
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 0.7Version 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
  • libgtextutils.so:biology/libgtextutils
libsbml API Library for Working with SBML File
5.18.0 search for ports that depend on this port Find issues related to this port Report an issue related to this port 5.18.0Version 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
  • libsbml.so:biology/libsbml
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 7.266Version 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 search for ports that depend on this port Find issues related to this port Report an issue related to this port 3.0Version 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: not specified in port
Dependency lines:
  • 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 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
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Port Added: 2001-08-06 10:07:46
License: not specified in port
Dependency lines:
  • migrate>0:biology/migrate
minc2 Medical Imaging NetCDF
2.2.00_9,1* search for ports that depend on this port Find issues related to this port Report an issue related to this port 2.2.00Version 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
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Port Added: 2006-04-30 12:09:06
Also Listed In: science
License: MIT
Dependency lines:
  • minc2>0:science/minc2
minimap2 Pairwise aligner for genomic and spliced nucleotide sequences
2.17 search for ports that depend on this port Find issues related to this port Report an issue related to this port 2.17Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
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* search for ports that depend on this port Find issues related to this port Report an issue related to this port 1.0.0Version of this port present on the latest quarterly branch.
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
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 search for ports that depend on this port Find issues related to this port Report an issue related to this port 5.8.2Version of this port present on the latest quarterly branch.
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 lines:
  • molden>0:biology/molden
mopac Semi-empirical (MNDO, etc.) molecular orbital calculation
7.1.15_8,1 search for ports that depend on this port Find issues related to this port Report an issue related to this port 7.1.15Version 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
License: GPLv2+
Dependency lines:
  • mopac>0:biology/mopac
mothur Software for bioinformatics of the microbial ecology community
1.43.0 search for ports that depend on this port Find issues related to this port Report an issue related to this port 1.43.0Version of this port present on the latest quarterly branch.
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2019-05-20 17:59:35
License: GPLv3
Dependency lines:
  • mothur>0:biology/mothur
mrbayes Bayesian inference of phylogeny
3.1.2_3 search for ports that depend on this port Find issues related to this port Report an issue related to this port 3.1.2Version of this port present on the latest quarterly branch.
Broken BROKEN: unfetchable
Ignore IGNORE: is marked as broken: unfetchable
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 lines:
  • mrbayes>0:biology/mrbayes
mummer Modular system for rapid whole genome alignment
4.0.0.b2.2_2 search for ports that depend on this port Find issues related to this port Report an issue related to this port 4.0.0.b2.2Version of this port present on the latest quarterly branch.
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2007-12-14 20:56:11
License: ART10
Dependency lines:
  • mummer>0:biology/mummer
muscle MUltiple Sequence Comparison by Log-Expectation
3.8.1551 search for ports that depend on this port Find issues related to this port Report an issue related to this port 3.8.31Version of this port present on the latest quarterly branch.
Maintainer: mzaki@e-mail.ne.jp search for ports maintained by this maintainer
Port Added: 2008-05-14 13:52:50
License: PD
Dependency lines:
  • muscle>0:biology/muscle
ncbi-blast+ NCBI implementation of Basic Local Alignment Search Tool
2.10.0 search for ports that depend on this port Find issues related to this port Report an issue related to this port 2.10.0Version of this port present on the latest quarterly branch.
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 lines:
  • ncbi-blast+>0:biology/ncbi-blast+
ncbi-cxx-toolkit NCBI C++ Toolkit
21.0.0_2 search for ports that depend on this port Find issues related to this port Report an issue related to this port 21.0.0Version of this port present on the latest quarterly branch.
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 lines:
  • ncbi-cxx-toolkit>0:biology/ncbi-cxx-toolkit
ncbi-toolkit NCBI development toolkit, including BLAST 2 and GenBank/Entrez support
2017.01.06_4 search for ports that depend on this port Find issues related to this port Report an issue related to this port 2017.01.06Version of this port present on the latest quarterly branch.
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 lines:
  • ncbi-toolkit>0:biology/ncbi-toolkit
nest Simulator for spiking neural network models
2.20.0* search for ports that depend on this port Find issues related to this port Report an issue related to this port 2.18.0Version of this port present on the latest quarterly branch.
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2019-05-11 20:30:18
Also Listed In: science
License: GPLv2
Dependency lines:
  • nest>0:science/nest
ngs-sdk Tools and libraries for using data in the INSDC Sequence Read Archives
2.10.2 search for ports that depend on this port Find issues related to this port Report an issue related to this port 2.10.0Version of this port present on the latest quarterly branch.
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
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 search for ports that depend on this port Find issues related to this port Report an issue related to this port 1.92Version of this port present on the latest quarterly branch.
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 lines:
  • p5-AcePerl>0:biology/p5-AcePerl
p5-Bio-ASN1-EntrezGene Regular expression-based Perl Parser for NCBI Entrez Gene
1.73_2,1 search for ports that depend on this port Find issues related to this port Report an issue related to this port 1.73Version of this port present on the latest quarterly branch.
Maintainer: sunpoet@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 lines:
  • p5-Bio-ASN1-EntrezGene>0:biology/p5-Bio-ASN1-EntrezGene
p5-Bio-Cluster BioPerl cluster modules
1.7.3_1 search for ports that depend on this port Find issues related to this port Report an issue related to this port 1.7.3Version of this port present on the latest quarterly branch.
Maintainer: sunpoet@FreeBSD.org search for ports maintained by this maintainer
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 search for ports that depend on this port Find issues related to this port Report an issue related to this port 1.007001Version of this port present on the latest quarterly branch.
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 lines:
  • p5-Bio-Coordinate>0:biology/p5-Bio-Coordinate
p5-Bio-DB-EMBL Database object interface for EMBL entry retrieval
1.7.4 search for ports that depend on this port Find issues related to this port Report an issue related to this port 1.7.4Version of this port present on the latest quarterly branch.
Maintainer: sunpoet@FreeBSD.org search for ports maintained by this maintainer
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 search for ports that depend on this port Find issues related to this port Report an issue related to this port 1.7.6Version of this port present on the latest quarterly branch.
Maintainer: sunpoet@FreeBSD.org search for ports maintained by this maintainer
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 search for ports that depend on this port Find issues related to this port Report an issue related to this port 1.17Version of this port present on the latest quarterly branch.
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 lines:
  • 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 2.11Version of this port present on the latest quarterly branch.
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 lines:
  • 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 1.6.905Version of this port present on the latest quarterly branch.
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 lines:
  • 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 2.0Version of this port present on the latest quarterly branch.
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 lines:
  • 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 0.10Version of this port present on the latest quarterly branch.
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 lines:
  • 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 2.40Version of this port present on the latest quarterly branch.
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 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 search for ports that depend on this port Find issues related to this port Report an issue related to this port 1.31Version of this port present on the latest quarterly branch.
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 lines:
  • 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 0.78Version of this port present on the latest quarterly branch.
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 lines:
  • 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 2.0.1Version of this port present on the latest quarterly branch.
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 lines:
  • 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 1.03Version of this port present on the latest quarterly branch.
Maintainer: wen@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2009-08-28 23:38:55
Also Listed In: perl5
License: ART10 GPLv1+
Dependency lines:
  • p5-Bio-SCF>0:biology/p5-Bio-SCF

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