BSD Portsbiology/hyphy 2.5.103 FreeBSD
Hypothesis testing using Phylogenies
- System
- FreeBSD
- Repository
- FreeBSD ports
- Maintainer
- [email protected]
- Last update
- Commit
86b1dc3ea7- License
- MIT
- Categories
- biology
- Package size
- 1422.4 KiB, 6769.6 KiB installed
Description
HyPhy is an open-source software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning. It features a rich scripting language for limitless customization of analyses. Additionally, HyPhy features support for parallel computing environments via message passing interface, MPI and it can be compiled as a shared library and called from other programming environments such as Python and R.
In the other systems
| System | Port | Version |
|---|---|---|
| FreeBSD | biology/hyphy | 2.5.103 |
| DragonFly | biology/hyphy | 2.5.70 |
| HardenedBSD | biology/hyphy | 2.5.101 |
| GhostBSD | biology/hyphy | 2.5.101 |
Install
Binary package:
pkg install hyphyFrom the ports tree:
cd /usr/ports/biology/hyphy/ && make install cleanTo depend on this port in another port's Makefile:
RUN_DEPENDS= hyphy>0:biology/hyphyPackages
The version each package repository carries. “-” means the repository builds no package of it, “n/a” that there is no such repository.
| Repository | aarch64 | amd64 | armv6 | armv7 | i386 |
|---|---|---|---|---|---|
| FreeBSD:14:latest | 2.5.101 | 2.5.103 | - | - | 2.5.103 |
| FreeBSD:14:quarterly | 2.5.101 | 2.5.101 | n/a | - | 2.5.101 |
| FreeBSD:15:latest | 2.5.103 | 2.5.103 | n/a | - | 2.5.77_1 |
| FreeBSD:15:quarterly | 2.5.101 | 2.5.101 | n/a | n/a | n/a |
| FreeBSD:16:latest | 2.5.101 | 2.5.103 | n/a | n/a | n/a |
| FreeBSD:16:quarterly | n/a | n/a | n/a | n/a | n/a |
Dependencies
As this port's Makefile names them.
Library 1
libcurl.so: ftp/curl
Test 1
bash: shells/bash
The full lists below include those, and their dependencies in turn.
Build dependencies 22
- archivers/brotli
- archivers/liblz4
- archivers/zstd
- devel/cmake-core
- devel/gettext-runtime
- devel/jsoncpp
- devel/libffi
- devel/libunistring
- devel/libuv
- devel/ninja
- devel/readline
- dns/libidn2
- dns/libpsl
- ftp/curl
- lang/python312
- math/mpdecimal
- ports-mgmt/pkg
- print/indexinfo
- security/libssh2
- security/rhash
- textproc/expat2
- www/libnghttp2
Run dependencies 10
No port depends on this one.
Configuration
Options name: biology_hyphy
| Option | Default | Description |
|---|---|---|
| AVX | off | Support for AVX (Advanced Vector Extensions) instructions |
| FMA3 | off | Support for FMA3 (Fused Multiply-Add) instructions on x86 |
| NEON | off | Support for NEON SIMD instructions on ARM |
| SSE4 | off | Support for SSE4 (Streaming SIMD Extensions) instructions |
| TARGET_NATIVE | off | Enable CPU-specific optimizations for the build machine |
- USES
- cmake:insource,testing localbase:ldflags
- Service scripts
- none
Files
pkg-plist 457
- bin/hyphy
- share/hyphy/GeneticCodes/Alt_Yeast_Nuclear.cod
- share/hyphy/GeneticCodes/Ascidian_mtDNA.cod
- share/hyphy/GeneticCodes/Blepharisma_Nuclear.cod
- share/hyphy/GeneticCodes/Ciliate.cod
- share/hyphy/GeneticCodes/Echinoderm_mtDNA.cod
- share/hyphy/GeneticCodes/Euplotid_Nuclear.cod
- share/hyphy/GeneticCodes/Flatworm_mtDNA.cod
- share/hyphy/GeneticCodes/Invertebrate_mtDNA.cod
- share/hyphy/GeneticCodes/Mold_mtDNA.cod
- share/hyphy/GeneticCodes/Thraustochytrium_mtDNA.cod
- share/hyphy/GeneticCodes/Vertebratemtdna.cod
- share/hyphy/GeneticCodes/Yeast_mtDNA.cod
- share/hyphy/README.md
- share/hyphy/SubstitutionClasses/AAEFV/Equal
- share/hyphy/SubstitutionClasses/AAEFV/Estimated
- share/hyphy/SubstitutionClasses/AAEFV/Observed In Data Set
- share/hyphy/SubstitutionClasses/AAEFV/Observed In Partition
- share/hyphy/SubstitutionClasses/CodonEFV/Equal
- share/hyphy/SubstitutionClasses/CodonEFV/Observed Codon
- share/hyphy/SubstitutionClasses/CodonEFV/Observed Nuc 3 params.
- share/hyphy/SubstitutionClasses/CodonEFV/Observed Nuc 9 params.
- share/hyphy/SubstitutionClasses/Heterogeneity/2 Bin Discrete
- share/hyphy/SubstitutionClasses/Heterogeneity/Beta
- share/hyphy/SubstitutionClasses/Heterogeneity/Beta-Gamma
- share/hyphy/SubstitutionClasses/Heterogeneity/General Discrete
- share/hyphy/SubstitutionClasses/Heterogeneity/Half Normal
- share/hyphy/SubstitutionClasses/Heterogeneity/Lognormal
- share/hyphy/SubstitutionClasses/NucEFV/Equal
- share/hyphy/SubstitutionClasses/NucEFV/Estimated
- share/hyphy/SubstitutionClasses/NucEFV/Observed In Data Set
- share/hyphy/SubstitutionClasses/NucEFV/Observed In Partition
- share/hyphy/SubstitutionClasses/aa.bf
- share/hyphy/SubstitutionClasses/codon.bf
- share/hyphy/SubstitutionClasses/dinuc.bf
- share/hyphy/SubstitutionClasses/nuc.bf
- share/hyphy/SubstitutionModels/Aminoacid/Dayhoff.mdl
- share/hyphy/SubstitutionModels/Aminoacid/EIAA.mdl
- share/hyphy/SubstitutionModels/Aminoacid/Fitness.mdl
- share/hyphy/SubstitutionModels/Aminoacid/Jones.mdl
- share/hyphy/SubstitutionModels/Aminoacid/mtREV.mdl
- share/hyphy/SubstitutionModels/Binary/F81.mdl
- share/hyphy/SubstitutionModels/Codon/GY94_3x4.mdl
- share/hyphy/SubstitutionModels/Codon/Lineage_MG94xHKY85.mdl
- share/hyphy/SubstitutionModels/Codon/MG94.mdl
- share/hyphy/SubstitutionModels/Codon/MG94REVOmegaCF3x4.mdl
- share/hyphy/SubstitutionModels/Codon/MG94_3x4.mdl
- share/hyphy/SubstitutionModels/Codon/MG94_HKY85x3_4.mdl
- share/hyphy/SubstitutionModels/Codon/MG94_REV_3x4.mdl
- share/hyphy/SubstitutionModels/Codon/MG94xHKY85_3x4_2Rates.mdl
- share/hyphy/SubstitutionModels/Codon/MG94xREV_3x4_DualRV.mdl
- share/hyphy/SubstitutionModels/Codon/MG94xREV_3x4_DualRV_GDD.mdl
- share/hyphy/SubstitutionModels/Codon/MG94xTN93_3x4.mdl
- share/hyphy/SubstitutionModels/Nucleotide/EFVEstimated.ibf
- share/hyphy/SubstitutionModels/Nucleotide/F81.mdl
- share/hyphy/SubstitutionModels/Nucleotide/HKY85.mdl
- share/hyphy/SubstitutionModels/Nucleotide/REV.mdl
- share/hyphy/SubstitutionModels/Nucleotide/REVBetaGamma.mdl
- share/hyphy/SubstitutionModels/Nucleotide/TrN.mdl
- share/hyphy/SubstitutionModels/User/Nucleotide/JC69
- share/hyphy/SubstitutionModels/User/Nucleotide/K2P
- share/hyphy/TemplateBatchFiles/2RatesAnalyses/GY94.mdl
- share/hyphy/TemplateBatchFiles/2RatesAnalyses/MG94GY94xREV_PARRIS_syn3.mdl
- share/hyphy/TemplateBatchFiles/2RatesAnalyses/MG94xREV.mdl
- share/hyphy/TemplateBatchFiles/2RatesAnalyses/MG94xREVxBivariate.mdl
- share/hyphy/TemplateBatchFiles/2RatesAnalyses/MG94xREVxBivariate_Multirate.mdl
- share/hyphy/TemplateBatchFiles/2RatesAnalyses/PARRIS_M1.def
- share/hyphy/TemplateBatchFiles/2RatesAnalyses/PARRIS_M2.def
- share/hyphy/TemplateBatchFiles/2RatesAnalyses/PARRIS_M3.def
- share/hyphy/TemplateBatchFiles/2RatesAnalyses/PARRIS_syn3.def
- share/hyphy/TemplateBatchFiles/2RatesAnalyses/PARRIS_synvar.def
- share/hyphy/TemplateBatchFiles/2RatesAnalyses/discreteGenerator.bf
- share/hyphy/TemplateBatchFiles/2RatesAnalyses/discreteGeneratorNoPS.bf
- share/hyphy/TemplateBatchFiles/2RatesAnalyses/gamma1.def
- share/hyphy/TemplateBatchFiles/2RatesAnalyses/gamma2+Inv.def
- share/hyphy/TemplateBatchFiles/2RatesAnalyses/gamma2.def
- share/hyphy/TemplateBatchFiles/AAModelComparison.bf
- share/hyphy/TemplateBatchFiles/AddABias.ibf
- share/hyphy/TemplateBatchFiles/AnalyzeCodonData.bf
- share/hyphy/TemplateBatchFiles/AnalyzeDiNucData.bf
- share/hyphy/TemplateBatchFiles/AnalyzeNucDataFreq.bf
- share/hyphy/TemplateBatchFiles/AnalyzeNucProtData.bf
- share/hyphy/TemplateBatchFiles/BGM.bf
- share/hyphy/TemplateBatchFiles/BivariateCodonRateAnalysis.bf
- share/hyphy/TemplateBatchFiles/BranchSiteREL.bf
- share/hyphy/TemplateBatchFiles/BranchSiteRELMultiModel.bf
- share/hyphy/TemplateBatchFiles/CleanGaps.bf
- share/hyphy/TemplateBatchFiles/CleanStopCodons.bf
- share/hyphy/TemplateBatchFiles/ClusterAnalysis.bf
- share/hyphy/TemplateBatchFiles/ClusterByDistanceRange.bf
- share/hyphy/TemplateBatchFiles/CodonBivariateRateProcessor.bf
- share/hyphy/TemplateBatchFiles/CodonModelCompare.bf
- share/hyphy/TemplateBatchFiles/CodonToProtein.bf
- share/hyphy/TemplateBatchFiles/ConvertDataFile.bf
- share/hyphy/TemplateBatchFiles/DirectionalREL.bf
- share/hyphy/TemplateBatchFiles/DistanceMatrix.bf
- share/hyphy/TemplateBatchFiles/Distances/CodonTools.def
- share/hyphy/TemplateBatchFiles/Distances/CodonTools2.def
- share/hyphy/TemplateBatchFiles/Distances/CodonToolsMain.def
- share/hyphy/TemplateBatchFiles/Distances/JC69
The first 100 are listed.
distinfo 1
| File | Size | SHA256 |
|---|---|---|
| veg-hyphy-2.5.103_GH0.tar.gz | 4.626617e+06 | e3602aa3add7f4d88c18038828bc49080a749dd377f9d41c92933fbf07d846c2 |