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Change Id->FreeBSD.
1999-08-25 06:58:03 +02:00
# $FreeBSD$
The new ports category "biology" starts here today. No Darwin jokes please!
1997-12-13 06:54:24 +01:00
#
Remove category pkg/COMMENT files in favour of a COMMENT variable in the category makefile. Submitted by: Matthew Seaman <m.seaman@infracaninophile.co.uk> PR: 59651
2004-04-02 09:29:48 +02:00
COMMENT = Biology
New port: biology/abyss: Assembly By Short Sequences: parallel, paired-end sequence assembler
2019-02-25 08:56:45 +01:00
SUBDIR += abyss
Initial import of artemis 4.0 Artemis is a DNA sequence viewer and annotation tool. PR: 32914 Submitted by: Camson <chuynh@biolateral.com.au>
2001-12-22 15:39:40 +01:00
SUBDIR += artemis
add avida 1.6.0 Avida is an auto-adaptive genetic system designed for ALife research PR: 37268 Submitted by: Jeremy Karlson <karlj000@unbc.ca>
2002-04-20 17:17:46 +02:00
SUBDIR += avida
Activate babel.
1997-12-21 22:58:57 +01:00
SUBDIR += babel
biology/bamtools: API and toolkit for handling BAM files Approved by: jrm Differential Revision: https://reviews.freebsd.org/D14877
2018-03-28 15:26:31 +02:00
SUBDIR += bamtools
New port: biology/bcftools BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. WWW: http://www.htslib.org/ PR: 199747 Submitted by: cartwright@asu.edu
2015-06-05 23:01:13 +02:00
SUBDIR += bcftools
The bedtools utilities are a suite of tools for performing a wide range of genomics analysis tasks. The most widely-used of these tools enable genome arithmetic, i.e., set theory on the genome. For example, with bedtools one can intersect, merge, count, complement, and shuffle genomic intervals from multiple files in common genomic formats such as BAM, BED, GFF/GTF, and VCF. Although each individual utility is designed to do a relatively simple task, e.g., intersect two interval files, more sophisticated analyses can be conducted by stringing together multiple bedtools operations on the command line or in shell scripts. WWW: http://bedtools.readthedocs.org/ PR: 204536 Submitted by: scottcheloha@gmail.com
2016-01-19 09:56:34 +01:00
SUBDIR += bedtools
The BioCocoa framework provides developers with the opportunity to add support for reading and writing BEAST, Clustal, EMBL, Fasta, GCG-MSF, GDE, Hennig86, NCBI, NEXUS, NONA, PDB, Phylip, PIR, Plain/Raw, Swiss-Prot and TNT files by writing only three lines of code. The framework is written in Cocoa (Objective-C). WWW: http://bioinformatics.org/biococoa/
2006-12-30 10:20:54 +01:00
SUBDIR += biococoa
New port: biology/bowtie. Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. WWW: http://bowtie-bio.sourceforge.net/index.shtml PR: 206939 Submitted by: Jason Bacon <bacon4000@gmail.com>
2016-03-05 14:21:26 +01:00
SUBDIR += bowtie
New port: biology/bowtie2. Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. This is Bowtie version 2, which will need to coexists with Bowtie 1 for the foreseeable future. Both are required by certain genomics pipelines, in some cases (e.g. Trinity) by the same pipeline. WWW: https://github.com/BenLangmead/bowtie2 PR: 207908 Submitted by: Jason Bacon <bacon4000@gmail.com>
2016-03-23 12:22:39 +01:00
SUBDIR += bowtie2
BWA is a program for aligning sequencing reads against a large reference genome (e.g. human genome). It has two major components, one for read shorter than 150bp and the other for longer reads. WWW: http://sourceforge.net/projects/bio-bwa/ PR: 203158 Submitted by: Jason Bacon <jwbacon@tds.net>
2015-09-25 20:39:36 +02:00
SUBDIR += bwa
[new port] biology/canu: Single molecule sequence assembler Approved by: jrm (mentor) or wen (mentor) Differential Revision: https://reviews.freebsd.org/D13574
2017-12-22 02:30:26 +01:00
SUBDIR += canu
CD-HIT is a very widely used program for clustering and comparing protein or nucleotide sequences. WWW: http://weizhong-lab.ucsd.edu/cd-hit/ PR: 203183 Submitted by: jwbacon@tds.net
2015-09-19 13:16:51 +02:00
SUBDIR += cd-hit
Fast indexing and retrieval of FASTA records from flat file data bases. WWW: http://sourceforge.net/projects/cdbfasta/ PR: 203233 Submitted by: Jason Bacon <jwbacon@tds.net>
2015-09-25 20:37:24 +02:00
SUBDIR += cdbfasta
New port: math/checkm: Quality assessment tool for the microbial genomes
2018-12-07 01:26:04 +01:00
SUBDIR += checkm
- Resurrect, update to version 1.5 (literally 1.50 since I wanted to avoid unnecessary PORTEPOCH bump) - Update MASTER_SITES and WWW line, provide backup download site - Come up with better port description - Reset maintainer to ports@ - Uphold CXX and CXXFLAGS - Clean up Makefile slightly - Don't install yet another copy of GPL and texts in French - Add SHA256 hash to distinfo
2006-01-19 20:47:59 +01:00
SUBDIR += chemeq
biology/clustal-omega: Multiple alignment of nucleic acid and protein, replaces clustalw Approved by: jrm Differential Revision: https://reviews.freebsd.org/D15516
2018-05-22 00:15:26 +02:00
SUBDIR += clustal-omega
- Sort category Makefiles Inspired by: Jason Harris <jharris@widomaker.com> Howto: http://twiki.cenkes.org/Cenkes/SortingCategoryMakefiles
2007-10-06 01:33:27 +02:00
SUBDIR += clustalw
New port: biology/consed viewing and editing workbench for sequence assembly Consed is a tool for viewing, editing, and finishing sequence assemblies. The port is constituted of 4 parts: biology/phred: base caller with quality evaluation biology/phrap: sequence assembler for shotgun sequencing biology/consed: workbench biology/phd2fasta: small utility All these can be used separately; however, most function of consed depends on the others. Although these programs are licensed freely for academic and nonprofit purposes, users have to contact the authors to get the softwares. Phred (including phd2fasta) and phrap are emailed, and consed can be downloaded to a restricted IP address. For commercial users, the licensing fee is ca. $10,000 at the time of writing. PR: ports/118548 Submitted by: Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp>
2008-05-24 09:00:37 +02:00
SUBDIR += consed
New port: biology/cytoscape: Software to visualize molecular interaction networks, gene expression
2018-07-03 10:42:54 +02:00
SUBDIR += cytoscape
biology/ddocent: Bash pipeline for RAD sequencing Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D15139
2018-04-20 03:34:05 +02:00
SUBDIR += ddocent
DNA query sequences against a protein reference database (BLASTP and BLASTX alignment mode). The speedup over BLAST is up to 20,000 on short reads at a typical sensitivity of 90-99% relative to BLAST depending on the data and settings. WWW: http://ab.inf.uni-tuebingen.de/software/diamond/ PR: 208998 Submitted by: jrm@ftfl.ca
2016-05-06 10:45:02 +02:00
SUBDIR += diamond
New port: biology/dsr-pdb: Simple C++ PDB reader (reads the protein description format)
2019-01-29 08:56:30 +01:00
SUBDIR += dsr-pdb
Add emboss, the European Molecular Biology Open Software Suite PR: ports/20317 Submitted by: Johann Visagie <johann@egenetics.com>
2000-07-31 21:13:54 +02:00
SUBDIR += emboss
New port: biology/exonerate: Generic tool for sequence alignment PR: 229180 Submitted by: Motomichi Matsuzaki <mzaki@niid.go.jp>
2018-07-13 09:02:16 +02:00
SUBDIR += exonerate
New port: biology/fasta, the FASTA2 suite of DNA and protein sequence search tools PR: 24715 Submitted by: Johann Visagie <johann@egenetics.com>
2001-02-11 17:24:18 +01:00
SUBDIR += fasta
- New port: biology/fasta3, which comprises the FASTA3 suite of DNA and protein sequence search programs - FASTA3 updates only some of the elements of FASTA2, which is why I have submitted ports of both versions (as biology/fasta and biology/fasta3) PR: 24716 Submitted by: Johann Visagie <johann@egenetics.com>
2001-02-11 17:28:59 +01:00
SUBDIR += fasta3
biology/fastahack: Utility for indexing and sequence extraction from FASTA files Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D15080
2018-04-16 16:50:46 +02:00
SUBDIR += fastahack
Initial import of fastDNAml Version 1.2.2 The faster variant of DNAML, makes phylogenetic trees using maximum likelihood PR: 21931 Submitted by: Motomichi Matsuzaki <mzaki@e-mail.ne.jp>
2000-10-12 14:31:13 +02:00
SUBDIR += fastdnaml
Simple and quick FastQ and FastA tool for file reading and conversion. WWW: https://github.com/fstrozzi/Fastool PR: 203293 Submitted by: Jason Bacon <jwbacon@tds.net>
2015-09-25 20:35:14 +02:00
SUBDIR += fastool
biology/fastp: Ultra-fast all-in-one FASTQ preprocessor fastp is a tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance.
2019-05-03 16:41:57 +02:00
SUBDIR += fastp
[new port] biology/fastqc: Quality control tool for high throughput sequence data Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D13304
2017-11-30 23:54:29 +01:00
SUBDIR += fastqc
FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. FastTree can handle alignments with up to a million of sequences in a reasonable amount of time and memory. WWW: http://www.microbesonline.org/fasttree/ PR: 203295 Submitted by: Jason Bacon <jwbacon@tds.net>
2015-09-25 20:34:29 +02:00
SUBDIR += fasttree
The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing. WWW: http://hannonlab.cshl.edu/fastx_toolkit/ PR: 203318 Submitted by: Jason Bacon <jwbacon@tds.net>
2015-09-25 20:33:18 +02:00
SUBDIR += fastx-toolkit
New port: biology/figtree: Graphical viewer of phylogenetic trees
2019-02-03 22:14:38 +01:00
SUBDIR += figtree
Add fluctuate 1.30, a program to fit population models.
2001-08-06 16:45:39 +02:00
SUBDIR += fluctuate
biology/freebayes: Bayesian haplotype-based polymorphism discovery and genotyping Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D15116
2018-04-20 02:07:27 +02:00
SUBDIR += freebayes
A new port garlic, free molecular viewer and editor, free molecular visualization program, protein structure, DNA structure, PDB, molecular rendering, biological macromolecule.
2003-07-28 08:38:37 +02:00
SUBDIR += garlic
New port: biology/gatk: Variant discovery in high-throughput sequencing data
2018-12-03 09:40:53 +01:00
SUBDIR += gatk
Add gff2ps 0.97b, converts gff-formated genomic data-sets to PostScript. PR: 32920 Submitted by: Camson Huynh <chuynh@biolateral.com.au>
2001-12-19 11:03:26 +01:00
SUBDIR += gff2ps
Add gmap 2006.04.21, a Genomic Mapping and Alignment Program for mRNA and EST Sequences. PR: ports/103651 Submitted by: Bob Zimmermann <rpz at cse.wustl.edu>
2006-09-29 06:05:55 +02:00
SUBDIR += gmap
Added gperiodic and xmolwt
1999-09-06 22:09:12 +02:00
SUBDIR += gperiodic
New port: biology/graphlan: High-quality circular representations of taxonomic, phylogenetic trees
2019-02-03 21:13:26 +01:00
SUBDIR += graphlan
Add grappa 1.0.2, Genome Rearrangements Analysis and Phylogeny Software. PR: 28541 Submitted by: dbader@eece.unm.edu
2001-07-04 10:39:40 +02:00
SUBDIR += grappa
New port: math/groopm: Metagenomic binning suite
2018-12-07 01:10:05 +01:00
SUBDIR += groopm
New port: biology/hisat2: Program for mapping next-generation sequencing reads Approved by: jrm (mentor, implicit)
2019-01-11 17:02:05 +01:00
SUBDIR += hisat2
Sort categories Makefiles.
2019-01-22 17:26:49 +01:00
SUBDIR += hmmer
HTSlib is an implementation of a unified C library for accessing common file formats, such as SAM, CRAM, VCF, and BCF, used for high-throughput sequencing data. It is the core library used by samtools and bcftools. WWW: http://www.htslib.org/ PR: 195591 Submitted by: Reed A. Cartwright <cartwright@asu.edu>
2014-12-14 23:35:07 +01:00
SUBDIR += htslib
New port, biology/hyphy: Hypothesis testing using Phylogenies WWW: http://www.hyphy.org/
2018-05-11 02:05:16 +02:00
SUBDIR += hyphy
New port: biology/igv: Visualization tool for genomic datasets
2018-06-26 01:56:00 +02:00
SUBDIR += igv
Add new port: biology/infernal Infernal is a tool for searching DNA sequence database for RNA structure and sequence similarities. The Rfam database of RNA families is based on Infernal, and we can search DNA sequences for structural homologs of Rfam families. WWW: http://eddylab.org/infernal/ PR: 228776 Submitted by: Motomichi Matsuzaki <mzaki@niid.go.jp>
2018-06-06 17:15:18 +02:00
SUBDIR += infernal
Io_lib is a library of file reading and writing code to provide a general purpose trace file (and Experiment File) reading interface. The programmer simply calls the (eg) read_reading to create a "Read" C structure with the data loaded into memory. It has been compiled and tested on a variety of unix systems, MacOS X and MS Windows. WWW: http://staden.sourceforge.net/ PR: ports/138254 Submitted by: Wen Heping <wenheping at gmail.com>
2009-08-29 01:34:20 +02:00
SUBDIR += iolib
New port, biology/iqtree: Efficient phylogenomic software WWW: http://www.iqtree.org/
2017-10-21 18:57:53 +02:00
SUBDIR += iqtree
Jalview is a multiple alignment editor written in Java. It is used widely in a variety of web pages (e.g. the EBI Clustalw server and the Pfam protein domain database) and is also available as a general purpose alignment editor. WWW: http://www.jalview.org PR: 93054 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar>
2006-02-13 10:42:13 +01:00
SUBDIR += jalview
Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence. JELLYFISH can count k-mers quickly by using an efficient encoding of a hash table and by exploiting the "compare-and-swap" CPU instruction to increase parallelism. WWW: http://www.genome.umd.edu/jellyfish.html PR: 207929 Submitted by: bacon4000@gmail.com
2016-03-24 14:53:06 +01:00
SUBDIR += jellyfish
[new port] biology/kallisto: Quantify abundances of transcripts from RNA-Seq data Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D13328
2017-12-02 21:44:28 +01:00
SUBDIR += kallisto
Add lagan 1.2, efficient tools for large-scale multiple alignments of genomic DNA. PR: ports/93058 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar>
2006-03-16 23:31:26 +01:00
SUBDIR += lagan
Add lamarc 2001.08.06, a package of programs for computing population parameters.
2001-08-07 10:17:58 +02:00
SUBDIR += lamarc
Gordon's text utilities. WWW: https://github.com/agordon/libgtextutils PR: 203309 Submitted by: Jason Bacon <jwbacon@tds.net>
2015-09-25 20:31:28 +02:00
SUBDIR += libgtextutils
LibSBML is an open-source programming library to help you read, write, manipulate, translate, and validate SBML files and data streams. It is not an application itself (though it does come with example programs), but rather a library you can embed in your own applications. LibSBML understands all Levels and Versions of SBML, as well as the SBML Layout proposal by Gauges, Rost, Sahle and Wegner. It's written in ISO C and C++ but can be used from all the languages listed in the right-hand box. WWW: http://www.sbml.org/ PR: ports/135022 Submitted by: Wen Heping <wenheping at gmail.com>
2009-05-29 01:36:10 +02:00
SUBDIR += libsbml
Folding@Home is a distributed computing project -- people from through out the world download and run software to band together to make one of the largest supercomputers in the world. Every computer makes the project closer to our goals. Folding@Home uses novel computational methods coupled to distributed computing, to simulate problems thousands to millions of times more challenging than previously achieved. WWW: http://folding.standford.edu PR: ports/101235 Submitted by: Yonatan <onatan@gmail.com>
2006-08-29 00:33:45 +02:00
SUBDIR += linux-foldingathome
Add mafft 5.734, multiple sequence alignments based on fast Fourier transform. PR: ports/93059 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar>
2006-03-15 11:41:16 +01:00
SUBDIR += mafft
MAPMAKER/EXP is a linkage analysis package designed to help construct primary linkage maps of markers segregating in experimental crosses. MAPMAKER/EXP performs full multipoint linkage analysis (simultaneous estimation of all recombination fractions from the primary data) for dominant, recessive, and co- dominant (e.g. RFLP-like) markers. MAPMAKER/EXP is an experimental-cross-only successor to the original MAPMAKER program. MAPMAKER/QTL is a companion program to MAPMAKER/EXP which allows one to map genes controlling polygenic quantitative traits in F2 intercrosses and BC1 backcrosses relative to a genetic linkage map. More information on MAPMAKER/QTL can be found in the technical report (included with MAPMAKER/QTL). WWW: http://www.broad.mit.edu/ftp/distribution/software/mapmaker3/ PR: ports/122452 Submitted by: Tassilo Philipp <tphilipp at potion-studios.com>
2008-04-06 06:49:05 +02:00
SUBDIR += mapm3
Add migrate 1.2, a program to estimate population sizes and migration rates.
2001-08-06 15:07:46 +02:00
SUBDIR += migrate
biology/minimap2: Pairwise aligner for genomic and spliced nucleotide sequences Minimap2 is a versatile sequence alignment program that aligns DNA or mRNA sequences against a large reference database.
2019-04-24 20:03:49 +02:00
SUBDIR += minimap2
Add platon and molden
1999-05-07 08:59:25 +02:00
SUBDIR += molden
Add mopac and psi88 (Move mopac and psi88 from misc to biology)
1999-05-06 10:18:35 +02:00
SUBDIR += mopac
MrBayes is a program for the Bayesian estimation of phylogeny. Bayesian inference of phylogeny is based upon a quantity called the posterior probability distribution of trees, which is the probability of a tree conditioned on the observations. The conditioning is accomplished using Bayes's theorem. The posterior probability distribution of trees is impossible to calculate analytically; instead, MrBayes uses a simulation technique called Markov chain Monte Carlo (or MCMC) to approximate the posterior probabilities of trees. WWW: http://mrbayes.csit.fsu.edu/ PR: ports/118542 Submitted by: mzaki at biol.s.u-tokyo.ac.jp
2007-12-15 16:13:41 +01:00
SUBDIR += mrbayes
MUMmer is a modular system for the rapid whole genome alignment of finished or draft sequence. This package provides an efficient suffix tree library, seed-and-extend alignment, SNP detection, repeat detection, and visualization tools. WWW: http://mummer.sourceforge.net/ PR: ports/118142 Submitted by: Tony Maher
2007-12-14 21:54:47 +01:00
SUBDIR += mummer
MUSCLE is multiple alignment software for protein and nucleotide sequences. The name stands for multiple sequence comparison by log-expectation. A range of options is provided that give you the choice of optimizing accuracy, speed, or some compromise between the two. Default parameters are those that give the best average accuracy in the published tests. MUSCLE can achieve both better average accuracy and better speed than CLUSTALW or T-Coffee, depending on the chosen options. Citation: Edgar, R. C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 32(5): 1792-1797. Edgar, R. C. (2004) MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5(1): 113. The NAR paper gives only a brief overview of the algorithm and implementation details. For a full discussion of the method and many of the non-default options that it offers, please see the BMC paper. WWW: http://www.drive5.com/muscle/ PR: ports/118460 Submitted by: Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp>
2008-05-14 15:51:50 +02:00
SUBDIR += muscle
Rename biology/ncbi-blast to biology/ncbi-blast+ Approved by: mentors (implicit)
2014-12-30 21:03:13 +01:00
SUBDIR += ncbi-blast+
New port: biology/ncbi-cxx-toolkit: NCBI C++ Toolkit
2018-10-08 09:54:49 +02:00
SUBDIR += ncbi-cxx-toolkit
New Port: biology/ncbi-toolkit National Center for Biotechnology Information (NCBI) Development Toolkit. PR: 22388 Submitted by: Tony Maher <tony.maher@ebioinformatics.com>
2000-10-29 14:56:24 +01:00
SUBDIR += ncbi-toolkit
New port: biology/ngs-sdk: Tools and libraries for using data in the INSDC Sequence Read Archives
2018-06-11 01:58:07 +02:00
SUBDIR += ngs-sdk
Add p5-AcePerl, a perl interface to the ACEDB genome database system PR: ports/20223 Submitted by: Johann Visagie <johann@egenetics.com>
2000-07-28 15:16:10 +02:00
SUBDIR += p5-AcePerl
Add p5-Bio-ASN1-EntrezGene, a Regular expression-based Perl Parser for NCBI Entrez Gene. PR: 87423 Submitted by: Mauricio Herrera Cuadra <mauricio@arareko.net> Approved by: novel (mentor) (implicit)
2005-10-15 22:09:50 +02:00
SUBDIR += p5-Bio-ASN1-EntrezGene
Add p5-Bio-Cluster 1.7.3 Bio::Cluster is the BioPerl cluster modules. Classes and modules here describe the basic structure for a cluster of BioPerl objects. WWW: https://metacpan.org/release/Bio-Cluster
2019-02-20 21:46:37 +01:00
SUBDIR += p5-Bio-Cluster
- Add p5-Bio-Coordinate 1.007001 Bio::Coordinate classes are used for working with various biological coordinate systems. See Bio::Coordinate::Collection and Bio::Collection::Pair for examples. WWW: http://search.cpan.org/dist/Bio-Coordinate/
2016-12-19 16:54:39 +01:00
SUBDIR += p5-Bio-Coordinate
Add p5-Bio-Das 1.02, client-side library for Distributed Genome Annotation System. PR: ports/76379 Submitted by: Razi Khaja <razi@genet.sickkids.on.ca>
2005-09-01 15:09:32 +02:00
SUBDIR += p5-Bio-Das
p5-Bio-Das-Lite is an implementation of a client for the DAS protocol (XML over HTTP primarily for biological-data). WWW: http://search.cpan.org/dist/Bio-Das-Lite/ Feature safe: yes
2010-03-01 10:16:25 +01:00
SUBDIR += p5-Bio-Das-Lite
Add p5-Bio-FeatureIO 1.6.905 Bio::FeatureIO is an iterator subsystem for genomic sequence features. Bio::FeatureIO is a handler module for the formats in the FeatureIO set (eg, Bio::FeatureIO::GFF). It is the officially sanctioned way of getting at the format objects, which most people should use. The Bio::FeatureIO system can be thought of like biological file handles. They are attached to filehandles with smart formatting rules (eg, GFF format, or BED format) and can either read or write feature objects (Bio::SeqFeature objects, or more correctly, Bio::FeatureHolderI implementing objects, of which Bio::SeqFeature is one such object). If you want to know what to do with a Bio::SeqFeatureI object, read Bio::SeqFeatureI. The idea is that you request a stream object for a particular format. All the stream objects have a notion of an internal file that is read from or written to. A particular FeatureIO object instance is configured for either input or output. A specific example of a stream object is the Bio::FeatureIO::gff object. WWW: http://search.cpan.org/dist/Bio-FeatureIO/
2017-09-15 21:17:17 +02:00
SUBDIR += p5-Bio-FeatureIO
Bio::GFF3 are low-level, fast functions for parsing GFF version 3 files. All they do is convert back and forth between low-level Perl data structures and GFF3 text. WWW: http://search.cpan.org/dist/Bio-GFF3/
2011-04-22 10:51:24 +02:00
SUBDIR += p5-Bio-GFF3
Bio::Glite is an interface to G-language Genome Analysis Environment through its REST web service (http://www.g-language.org). This module allows almost everything G-language GAE can do, without installing all necessary tookits and modules. Advantage of this module over the standard installation of G-language GAE package is: 1. Easy installation from CPAN 2. Extremely light-weight (less than 1000 lines of code) 3. Does not require much CPU/RAM (all calculation is done on the cloud) Disadvantages includes: 1. Slower analysis speed 2. Internet connection is required 3. No other software interfaces such as the G-language Shell WWW: http://search.cpan.org/dist/Bio-Glite/ PR: ports/133273 Submitted by: Wen Heping <wenheping at gmail.com>
2009-04-02 20:24:59 +02:00
SUBDIR += p5-Bio-Glite
p5-Bio-Graphics is a simple GD-based renderer (diagram drawer) for DNA and protein sequences. WWW: http://search.cpan.org/dist/Bio-Graphics/ PR: ports/132088 Submitted by: Wen Heping <wenheping at gmail.com>
2009-03-10 19:50:49 +01:00
SUBDIR += p5-Bio-Graphics
p5-Bio-MAGETAB contains the core MAGE-TAB Utilities Perl modules. This is a beta release. All functions have now been implemented and most have test suites; the exceptions include the modules involved in export of MAGE-TAB documents, which are still a little experimental in nature. The API is mostly finalised (and fully documented), but some details may yet change where necessary to improve usability. WWW: http://search.cpan.org/dist/Bio-MAGETAB/ PR: ports/136021 Submitted by: Wen Heping <wenheping at gmail.com>
2009-07-01 11:03:28 +02:00
SUBDIR += p5-Bio-MAGETAB
Bio::NEXUS package provides an object-oriented, Perl-based applications programming interface (API) to the NEXUS file format of Maddison, et al., 1997 (Syst. Biol. 46:590-621). NEXUS is a powerful and extensible format designed for use in evolutionary analysis, including the analysis of molecular sequence data as well as classical morphological and life-history data. NEXUS is the input or output format for software such as PAUP*, MacClade, Mesquite, SIMMAP, MrBayes, Nexplorer, and so on. This package also contains the demonstration applications nexplot.pl (plot character data with a tree) and nextool.pl (allowing programmatic editing, e.g., selecting particular clades or subsets of data). WWW: http://search.cpan.org/dist/Bio-NEXUS/ PR: ports/137983 Submitted by: Wen Heping <wenheping at gmail.com>
2009-08-22 22:39:51 +02:00
SUBDIR += p5-Bio-NEXUS
Adding port biology/p5-Bio-Phylo, Phylogenetic analysis using perl. Approved by: tobez (implicit)
2006-05-13 18:48:15 +02:00
SUBDIR += p5-Bio-Phylo
Bio::SCF module allows you to read and update (in a restricted way) SCF chromatographic sequence files. It is an interface to Roger Staden's io-lib. See the installation directions for further instructions. WWW: http://search.cpan.org/dist/Bio-SCF/ PR: ports/138263 Submitted by: Wen Heping <wenheping at gmail.com>
2009-08-29 01:36:09 +02:00
SUBDIR += p5-Bio-SCF
- Move biology/p5-bioperl to biology/p5-BioPerl - Sort *_DEPENDS - Bump PORTREVISION for dependent ports
2016-12-18 16:25:04 +01:00
SUBDIR += p5-BioPerl
- Move biology/p5-bioperl-run to biology/p5-BioPerl-Run - Sort *_DEPENDS - Add NO_ARCH - Bump PORTREVISION for biology/p5-bioperl renaming
2016-12-18 16:25:44 +01:00
SUBDIR += p5-BioPerl-Run
[new port] biology/p5-TrimGalore: Wrapper around Cutadapt and FastQC for adapter and quality trimming Approved by: jrm (mentor) Differential Revision: D13400
2017-12-09 14:23:32 +01:00
SUBDIR += p5-TrimGalore
New port: biology/p5-transdecoder TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks. WWW: http://transdecoder.github.io/ PR: 207993 Submitted by: Jason Bacon <bacon4000@gmail.com>
2016-03-16 21:12:32 +01:00
SUBDIR += p5-transdecoder
Activating the chemeq, clustalw, paml, and phylip ports.
2000-07-10 05:26:57 +02:00
SUBDIR += paml
biology/pbbam: PacBio BAM C++ library, with SWIG bindings Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D15154
2018-04-23 18:08:21 +02:00
SUBDIR += pbbam
biology/pbcopper: Core C++ library for Pacific Biosciences tools Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D15171
2018-04-23 18:23:53 +02:00
SUBDIR += pbcopper
biology/pbseqan: Pacific Biosciences patched and stripped down SeqAn Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D15152
2018-04-21 19:21:30 +02:00
SUBDIR += pbseqan
biology/pear-merger: Memory-efficient and accurate paired-end read merger Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D14959
2018-04-04 19:21:39 +02:00
SUBDIR += pear-merger
New port: biology/consed viewing and editing workbench for sequence assembly Consed is a tool for viewing, editing, and finishing sequence assemblies. The port is constituted of 4 parts: biology/phred: base caller with quality evaluation biology/phrap: sequence assembler for shotgun sequencing biology/consed: workbench biology/phd2fasta: small utility All these can be used separately; however, most function of consed depends on the others. Although these programs are licensed freely for academic and nonprofit purposes, users have to contact the authors to get the softwares. Phred (including phd2fasta) and phrap are emailed, and consed can be downloaded to a restricted IP address. For commercial users, the licensing fee is ca. $10,000 at the time of writing. PR: ports/118548 Submitted by: Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp>
2008-05-24 09:03:23 +02:00
SUBDIR += phrap
New port: biology/consed viewing and editing workbench for sequence assembly Consed is a tool for viewing, editing, and finishing sequence assemblies. The port is constituted of 4 parts: biology/phred: base caller with quality evaluation biology/phrap: sequence assembler for shotgun sequencing biology/consed: workbench biology/phd2fasta: small utility All these can be used separately; however, most function of consed depends on the others. Although these programs are licensed freely for academic and nonprofit purposes, users have to contact the authors to get the softwares. Phred (including phd2fasta) and phrap are emailed, and consed can be downloaded to a restricted IP address. For commercial users, the licensing fee is ca. $10,000 at the time of writing. PR: ports/118548 Submitted by: Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp>
2008-05-24 09:04:45 +02:00
SUBDIR += phred
Activating the chemeq, clustalw, paml, and phylip ports.
2000-07-10 05:26:57 +02:00
SUBDIR += phylip
PhyML is a software that estimates maximum likelihood phylogenies from alignments of nucleotide or amino acid sequences. It provides a wide range of options that were designed to facilitate standard phylogenetic analyses. The main strengths of PhyML lies in the large number of substitution models coupled to various options to search the space of phylogenetic tree topologies, going from very fast and efficient methods to slower but generally more accurate approaches. It also implements two methods to evaluate branch supports in a sound statistical framework (the non-parametric bootstrap and the approximate likelihood ratio test). PhyML was designed to process moderate to large data sets. In theory, alignments with up to 4,000 sequences 2,000,000 character-long can analyzed. In practice however, the amount of memory required to process a data set is proportional of the product of the number of sequences by their length. Hence, a large number of sequences can only be processed provided that they are short. Also, PhyML can handle long sequences provided that they are not numerous. With most standard personal computers, the "comfort zone" for PhyML generally lies around 3 to 500 sequences less than 2,000 character long. WWW: http://code.google.com/p/phyml/ PR: 136877 Submitted by: Ben Allen <ben@sysadminschronicles.com>
2009-07-21 03:10:13 +02:00
SUBDIR += phyml
Add new ports biology/plink [1] and biology/plinkseq [2]: PLINK is a free, open-source whole genome association analysis toolset. PLINK/SEQ is an open-source C/C++ library for working with human genetic variation data. PR: ports/171918 [1] PR: ports/171922 [2] Submitted by: Jason Bacon <jwbacon at tds.net>
2012-09-27 11:59:25 +02:00
SUBDIR += plinkseq
add primer3 0.9 Primer3 helps to choose primers for PCR reactions PR: 35298 Submitted by: Tony Maher <tonym@biolateral.com.au>
2002-09-17 17:31:09 +02:00
SUBDIR += primer3
New port: biology/prodigal: Protein-coding gene prediction for prokaryotic genomes
2019-02-03 19:08:14 +01:00
SUBDIR += prodigal
New port: biology/prodigy-lig: Prediction of protein-small molecule binding affinities
2019-02-03 19:49:23 +01:00
SUBDIR += prodigy-lig
Add protomol 2.0.3, OO, component based, framework for molecular dynamics (MD) simulations. PR: 95123 Submitted by: Sangwoo Shim <sangwoos@gmail.com>
2006-05-05 22:09:54 +02:00
SUBDIR += protomol
Add mopac and psi88 (Move mopac and psi88 from misc to biology)
1999-05-06 10:18:35 +02:00
SUBDIR += psi88
New port: biology/py-Genesis-PyAPI: API for the Genesis platform for genetics information processing
2018-06-13 03:46:03 +02:00
SUBDIR += py-Genesis-PyAPI
The BIOM file format (canonically pronounced biome) is designed to be a general-use format for representing biological sample by observation contingency tables. BIOM is a recognized standard for the Earth Microbiome Project and is a Genomics Standards Consortium supported project. The BIOM format is designed for general use in broad areas of comparative -omics. For example, in marker-gene surveys, the primary use of this format is to represent OTU tables: the observations in this case are OTUs and the matrix contains counts corresponding to the number of times each OTU is observed in each sample. With respect to metagenome data, this format would be used to represent metagenome tables: the observations in this case might correspond to SEED subsystems, and the matrix would contain counts corresponding to the number of times each subsystem is observed in each metagenome. Similarly, with respect to genome data, this format may be used to represent a set of genomes: the observations in this case again might correspond to SEED subsystems, and the counts would correspond to the number of times each subsystem is observed in each genome. WWW: http://biom-format.org/ PR: 209193 Submitted by: Joseph Mingrone
2016-05-09 18:37:44 +02:00
SUBDIR += py-biom-format
Add py-biopython, is a collection of Python packages and modules created by the Biopython Project, intended to provide the basis for building bioinformatics applications in the Python language. PR: ports/20260 Submitted by: Johann Visagie <johann@egenetics.com>
2000-07-31 14:12:24 +02:00
SUBDIR += py-biopython
bx-python is a python library and associated set of scripts to allow for rapid implementation of genome scale analyses. The library contains a variety of useful modules, but the particular strengths are: Classes for reading and working with genome-scale multiple local alignments (in MAF, AXT, and LAV formats). Generic data structure for indexing on disk files that contain blocks of data associated with intervals on various sequences (used, for example, to provide random access to individual alignments in huge files; optomized for use over network filesystems). Data structures for working with intervals on sequences: * "Binned bitsets" which act just like chromosome sized bit arrays, but lazily allocate regions and allow large blocks of all set or all unset bits to be stored compactly * "Intersecter" for performing fast intersection tests that preserve both query and target intervals and associated annotation WWW: https://github.com/bxlab/bx-python PR: 218757 Submitted by: Yuri Victorovich <yuri@rawbw.com>
2017-05-06 08:07:03 +02:00
SUBDIR += py-bx-python
[new port] biology/py-cutadapt: Finds and removes adapter sequences, primers, po ly-A tails, etc Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D13294
2017-11-29 23:17:43 +01:00
SUBDIR += py-cutadapt
biology/py-dnaio: Read and write FASTQ and FASTA Factored out of py-cutadapt Reviewed by: jrm
2019-03-24 20:40:26 +01:00
SUBDIR += py-dnaio
New port: biology/py-fastTSNE: Fast, parallel implementations of t-SNE
2018-12-15 09:58:05 +01:00
SUBDIR += py-fastTSNE
New port: biology/py-gffutils: Work with GFF and GTF files in a flexible database framework
2018-10-19 04:06:53 +02:00
SUBDIR += py-gffutils
New port: biology/py-gtfparse: Parsing tools for GTF (gene transfer format) files
2018-10-19 04:03:40 +02:00
SUBDIR += py-gtfparse
New port: biology/py-loompy: Work with .loom files for single-cell RNA-seq data
2018-09-21 10:04:50 +02:00
SUBDIR += py-loompy
[new port] biology/py-macs2: Analysis of chromatin immunoprecipitation (ChIP) sequences Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D13322
2017-12-02 21:46:28 +01:00
SUBDIR += py-macs2
New port: biology/py-orange3-bioinformatics: Orange add-on providing common functionality for bioinformatics
2018-06-14 08:25:21 +02:00
SUBDIR += py-orange3-bioinformatics
New port: biology/py-orange3-single-cell: Orange add-on for gene expression of single cell data
2018-08-07 09:50:40 +02:00
SUBDIR += py-orange3-single-cell
New port: biology/py-pyfaidx: Efficient pythonic random access to fasta subsequences
2018-10-19 04:05:37 +02:00
SUBDIR += py-pyfaidx
pysam is a lightweight wrapper of the htslib C-API and provides facilities to read and write SAM/BAM/VCF/BCF/BED/GFF/GTF/FASTA/FASTQ files as well as access to the command line functionality of the samtools and bcftools packages. The module supports compression and random access through indexing. This module provides a low-level wrapper around the htslib C-API as using cython and a high-level API for convenient access to the data within standard genomic file formats. WWW: https://pypi.python.org/pypi/pysam PR: 218745 Submitted by: Yuri Victorovich <yuri@rawbw.com>
2017-05-06 08:05:24 +02:00
SUBDIR += py-pysam
New port: biology/py-xenaPython: API for Xena Hub to access genetic information shared through the hub
2019-04-12 19:01:10 +02:00
SUBDIR += py-xenaPython
PyCogent is a software library for genomic biology. It is a fully integrated and thoroughly tested framework for: controlling third-party applications; devising workflows; querying databases; conducting novel probabilistic analyses of biological sequence evolution; and generating publication quality graphics. It is distinguished by many unique built-in capabilities (such as true codon alignment) and the frequent addition of entirely new methods for the analysis of genomic data. WWW: http://pycogent.sourceforge.net/ PR: ports/135863 Submitted by: Wen Heping <wenheping at gmail.com>
2009-06-22 14:46:56 +02:00
SUBDIR += pycogent
pyfasta is a python module for fast, memory-efficient, pythonic access to fasta sequence files. WWW: http://bitbucket.org/brentp/biostuff/src/
2009-11-18 06:53:17 +01:00
SUBDIR += pyfasta
python-nexus is a generic nexus (phylogenetics) file format(.nex, .trees) reader for python. WWW: http://simon.net.nz/articles/python-nexus
2009-12-29 14:39:14 +01:00
SUBDIR += python-nexus
biology/rainbow: Efficient clustering and assembling of short reads Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D14924
2018-04-02 18:50:46 +02:00
SUBDIR += rainbow
Add recombine 1.40, a program to fit population models across sites.
2001-08-06 16:49:53 +02:00
SUBDIR += recombine
Add ruby-bio (BioRuby), an integrated environment for Bioinformatics written in Ruby.
2001-10-24 08:21:52 +02:00
SUBDIR += ruby-bio
Move devel/rubygem-bio to biology/rubygem-bio
2017-02-05 05:26:56 +01:00
SUBDIR += rubygem-bio
Samtools implements various utilities for post-processing alignments in the SAM, BAM, and CRAM formats, including indexing, variant calling (in conjunction with bcftools), and a simple alignment viewer. WWW: http://www.htslib.org/ PR: 195592 Submitted by: Reed A. Cartwright <cartwright@asu.edu>
2014-12-15 22:59:19 +01:00
SUBDIR += samtools
Activate seaview.
1997-12-21 23:05:43 +01:00
SUBDIR += seaview
SeqAn is an open source C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data. The library is licensed under the 3-clause BSD license except the applications which are GPL. WWW: http://www.seqan.de/ PR: 167571 Submitted by: Hannes <h2+fbsdports@fsfe.org>
2012-06-06 19:51:33 +02:00
SUBDIR += seqan
New port: biology/seqan-apps SeqAn is an open source C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data. This port contains applications built on SeqAn and developed within the SeqAn project. Among them are famous read mappers like RazerS and Yara, as well as many other tools. Some applications are packaged seperately and the library can be found at biology/seqan. WWW: http://www.seqan.de/ PR: 204127 Submitted by: Hannes Hauswedell <h2+fbsdports@fsfe.org>
2016-05-10 02:52:04 +02:00
SUBDIR += seqan-apps
biology/seqan: update 1.3.1 -> 2.1.1 biology/seqan1: create port from current SeqAn 1.3.1 for legacy usage UPDATING: document SeqAn updates and seqan1 port for legacy usage PR: 204127 Submitted by: Hannes Hauswedell <h2+fbsdports@fsfe.org>
2016-05-10 03:05:23 +02:00
SUBDIR += seqan1
Add seqio 1.2.2, a set of C functions which can read/write biological sequence files. PR: 29922 Submitted by: Tony Maher <tonym@biolateral.com.au>
2001-08-22 14:07:26 +02:00
SUBDIR += seqio
biology/seqtk: Tool for processing sequences in FASTA/FASTQ format Approved by: jrm Differential Revision: https://reviews.freebsd.org/D14954
2018-04-03 22:57:05 +02:00
SUBDIR += seqtk
biology/seqtools: Tools for visualising sequence alignments Blixem is an interactive browser of pairwise alignments that have been stacked up in a "master-slave" multiple alignment; it is not a 'true' multiple alignment but a 'one-to-many' alignment. Belvu is a multiple sequence alignment viewer and phylogenetic tool. Dotter is a graphical dot-matrix program for detailed comparison of two sequences. WWW: http://www.sanger.ac.uk/resources/software/seqtools/ PR: ports/183801 Submitted by: Kurt Jaeger <fbsd-ports opsec.eu>
2013-11-10 12:01:02 +01:00
SUBDIR += seqtools
Add sim4, an implementation of the sim4 algorithm for aligning expressed DNA with genomic sequences PR: ports/20219 Submitted by: Johann Visagie <johann@egenetics.com>
2000-07-27 16:33:00 +02:00
SUBDIR += sim4
New port: biology/slclust. Slclust is a utility that performs single-linkage clustering with the option of applying a Jaccard similarity coefficient to break weakly bound clusters into distinct clusters. WWW: http://sourceforge.net/projects/slclust/ PR: 207997 Submitted by: Jason Bacon <bacon4000@gmail.com>
2016-03-23 12:00:44 +01:00
SUBDIR += slclust
biology/smithwaterman: Smith-waterman-gotoh alignment algorithm Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D15072
2018-04-15 19:45:52 +02:00
SUBDIR += smithwaterman
biology/stacks: Software pipeline for building loci from short-read sequences Reviewed by: mat Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D14885
2018-03-31 15:16:05 +02:00
SUBDIR += stacks
biology/star: Spliced Transcripts Alignment to a Reference STAR is an extremely fast RNA-seq aligner, an alternative to tophat2, hisat2, bowtie, subread, etc.
2019-04-21 22:30:55 +02:00
SUBDIR += star
New port: biology/stringtie: Transcript assembly and quantification for RNA-seq PR: 229480 Submitted by: Motomichi Matsuzaki <mzaki@niid.go.jp>
2018-07-11 23:32:39 +02:00
SUBDIR += stringtie
Add tRNAscan-SE 1.21, an improved tool for transfer RNA detection. PR: 33853 Submitted by: chuynh@biolateral.com.au
2002-03-27 15:18:49 +01:00
SUBDIR += tRNAscan-SE
Add t_coffee 1.37, a multiple DNA or protein sequence alignment package.
2002-01-25 15:58:16 +01:00
SUBDIR += t_coffee
biology/tabixpp: C++ wrapper to tabix indexer Reviewed by: mat Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D14977
2018-04-15 01:52:16 +02:00
SUBDIR += tabixpp
add treepuzzle 5.1 Maximum likelihood phylogeny reconstruction using quartets PR: 45241 Submitted by: Jan Lentfer <lentferj@neslonek.bio.tu-darmstadt.de>
2002-11-20 09:54:10 +01:00
SUBDIR += treepuzzle
biology/trimadap: Trim adapter sequences from Illumina data Reviewed by: mat Approved by: jrm Differential Revision: https://reviews.freebsd.org/D14935
2018-04-03 20:23:54 +02:00
SUBDIR += trimadap
Trimmomatic performs a variety of useful trimming tasks for illumina NGS paired-end and single ended data. WWW: http://www.usadellab.org/cms/?page=trimmomatic PR: 208044 Submitted by: bacon4000@gmail.com
2016-03-17 09:21:14 +01:00
SUBDIR += trimmomatic
Add Unipro UGENE, a free open-source crowss-platform bioinformatics software. PR: ports/173387 Submitted by: Hannes Hauswedell
2013-02-23 05:50:48 +01:00
SUBDIR += ugene
biology/unanimity: Pacific Biosciences consensus library and applications Reviewed by: jrm Differential Revision: https://reviews.freebsd.org/D15172
2018-04-24 16:16:46 +02:00
SUBDIR += unanimity
biology/vcflib: C++ library and CLI tools for parsing and manipulating VCF files Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D15109
2018-04-17 05:11:39 +02:00
SUBDIR += vcflib
Regular sorting of categories Makefiles. Sponsored by: Absolight
2018-08-08 14:26:27 +02:00
SUBDIR += vcftools
Velvet is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454, developed by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute (EMBL-EBI). Citation: Velvet: algorithms for de novo short read assembly using de Bruijn graphs. D.R. Zerbino and E. Birney. Genome Research 18: 821-829 (2008) WWW: http://www.ebi.ac.uk/~zerbino/velvet/ PR: 140147 Submitted by: Motomichi Matsuzaki <mzaki@m.u-tokyo.ac.jp>
2009-11-07 02:23:59 +01:00
SUBDIR += velvet
biology/vsearch: Versatile open-source tool for metagenomics VSEARCH supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, rereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting. It also supports FASTQ file analysis, filtering, conversion and merging of paired-end reads. The aim of this project is to create an alternative to the USEARCH tool developed by Robert C. Edgar (2010).
2019-05-09 23:28:49 +02:00
SUBDIR += vsearch
"Wise2 is package that is focused on comparing DNA sequences at the level of its conceptual translation, regardless of sequencing error and introns."
2002-09-10 15:58:40 +02:00
SUBDIR += wise
The new ports category "biology" starts here today. No Darwin jokes please!
1997-12-13 06:54:24 +01:00
.include <bsd.port.subdir.mk>
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