BSD Portsbiology/paml 4.10.10 FreeBSD
Phylogenetic Analysis by Maximum Likelihood (PAML)
- System
- FreeBSD
- Repository
- FreeBSD ports
- Maintainer
- [email protected]
- License
- GPLv3
- Categories
- biology
- Package size
- 3379.2 KiB, 13047.3 KiB installed
Description
Phylogenetic Analysis by Maximum Likelihood (PAML)
PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. It is not good for tree making. It may be used to estimate parameters and test hypotheses for the study the evolutionary process using trees reconstructed with programs such as PAUP*, PHYLIP, MOLPHY, PhyML, or RaxML.
In the other systems
| System | Port | Version |
|---|---|---|
| FreeBSD | biology/paml | 4.10.10 |
| DragonFly | biology/paml | 4.10.7 |
| HardenedBSD | biology/paml | 4.10.10 |
| GhostBSD | biology/paml | 4.10.10 |
Install
Binary package:
pkg install pamlFrom the ports tree:
cd /usr/ports/biology/paml/ && make install cleanTo depend on this port in another port's Makefile:
RUN_DEPENDS= paml>0:biology/pamlPackages
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 | 4.10.10 | 4.10.10 | 4.10.6 | 4.10.9 | 4.10.10 |
| FreeBSD:14:quarterly | 4.10.10 | 4.10.10 | n/a | 4.10.9 | 4.10.10 |
| FreeBSD:15:latest | 4.10.10 | 4.10.10 | n/a | 4.10.9 | 4.10.9 |
| FreeBSD:15:quarterly | 4.10.10 | 4.10.10 | n/a | n/a | n/a |
| FreeBSD:16:latest | 4.10.10 | 4.10.10 | n/a | n/a | n/a |
| FreeBSD:16:quarterly | n/a | n/a | n/a | n/a | n/a |
Dependencies
The Makefile names none itself; they come from USES and USE_*.
The full lists below include those, and their dependencies in turn.
Build dependencies 3
No port depends on this one.
Configuration
Options name: biology_paml
| Option | Default | Description |
|---|---|---|
| DOCS | off | Build and/or install documentation |
| EXAMPLES | off | Build and/or install examples |
- USES
- dos2unix gmake
- Service scripts
- none
Files
pkg-plist 217
- bin/baseml
- bin/basemlg
- bin/chi2
- bin/codeml
- bin/evolver
- bin/evolverNSbranches
- bin/evolverNSbranchsites
- bin/evolverNSsites
- bin/infinitesites
- bin/mcmctree
- bin/pamp
- bin/yn00
- share/doc/paml/MCMCtree.Tutorials.pdf
- share/doc/paml/README.md
- share/doc/paml/pamlDOC.pdf
- share/doc/paml/pamlFAQs.pdf
- share/doc/paml/pamlHistory.txt
- share/examples/paml/3s.trees
- share/examples/paml/4s.trees
- share/examples/paml/5s.trees
- share/examples/paml/6s.trees
- share/examples/paml/9s.trees
- share/examples/paml/CladeModelCD/ECP_EDN_15.nuc
- share/examples/paml/CladeModelCD/PAMLCladeModelCDnotes.pdf
- share/examples/paml/CladeModelCD/codeml.CladeC.ctl
- share/examples/paml/CladeModelCD/codeml.CladeD.ctl
- share/examples/paml/CladeModelCD/tree.txt
- share/examples/paml/DatingSoftBound/BF.Clock23.xlsx
- share/examples/paml/DatingSoftBound/BFdriverDOC.pdf
- share/examples/paml/DatingSoftBound/FixedDsClock23.txt
- share/examples/paml/DatingSoftBound/README.BayesFactor.txt
- share/examples/paml/DatingSoftBound/README.txt
- share/examples/paml/DatingSoftBound/bf1/mcmctree.ctl
- share/examples/paml/DatingSoftBound/bf2/mcmctree.ctl
- share/examples/paml/DatingSoftBound/mcmctree.Infinitesites.ctl
- share/examples/paml/DatingSoftBound/mcmctree.ctl
- share/examples/paml/DatingSoftBound/mtCDNApri.trees
- share/examples/paml/DatingSoftBound/mtCDNApri123.txt
- share/examples/paml/GeneticCode.txt
- share/examples/paml/HIVNSsites/HIVenvSweden.trees
- share/examples/paml/HIVNSsites/HIVenvSweden.txt
- share/examples/paml/HIVNSsites/HIVenvSweden4s.trees
- share/examples/paml/HIVNSsites/HIVenvSweden4s.txt
- share/examples/paml/HIVNSsites/README.txt
- share/examples/paml/HIVNSsites/codeml.ctl
- share/examples/paml/MCaa.dat
- share/examples/paml/MCaa.txt
- share/examples/paml/MCbase.dat
- share/examples/paml/MCbase.txt
- share/examples/paml/MCbaseRandomTree.dat
- share/examples/paml/MCbaseRandomTree.txt
- share/examples/paml/MCcodon.dat
- share/examples/paml/MCcodon.txt
- share/examples/paml/MHC.Swanson2002MBE/README.txt
- share/examples/paml/MHC.Swanson2002MBE/bigmhc.phy
- share/examples/paml/MHC.Swanson2002MBE/bigmhc.trees
- share/examples/paml/MHC.Swanson2002MBE/codeml.ctl
- share/examples/paml/MouseLemurs/MouseLemurs.aa
- share/examples/paml/MouseLemurs/MouseLemurs.nuc
- share/examples/paml/MouseLemurs/MouseLemurs.trees
- share/examples/paml/MouseLemurs/MouseLemurs123.nuc
- share/examples/paml/MouseLemurs/README.txt
- share/examples/paml/MouseLemurs/README2.txt
- share/examples/paml/MouseLemurs/aaml.ctl
- share/examples/paml/MouseLemurs/aaml2.ctl
- share/examples/paml/MouseLemurs/baseml.ctl
- share/examples/paml/MouseLemurs/baseml2.ctl
- share/examples/paml/MouseLemurs/codeml.ctl
- share/examples/paml/MouseLemurs/codonml.ctl
- share/examples/paml/MouseLemurs/codonml2.ctl
- share/examples/paml/MouseLemurs/mtmam.dat
- share/examples/paml/README.txt
- share/examples/paml/Technical/Pt/eigenQREV.pdf
- share/examples/paml/Technical/Pt/testPMat.c
- share/examples/paml/Technical/Simulation/Codon/MCcodonNSbranches.dat
- share/examples/paml/Technical/Simulation/Codon/MCcodonNSbranchsites.dat
- share/examples/paml/Technical/Simulation/Codon/MCcodonNSclade.dat
- share/examples/paml/Technical/Simulation/Codon/MCcodonNSsites.dat
- share/examples/paml/Technical/Simulation/Codon/PositiveSites.c
- share/examples/paml/Technical/Simulation/Codon/README.txt
- share/examples/paml/Technical/Simulation/Codon/codeml.ctl
- share/examples/paml/Technical/Simulation/multiruns.c
- share/examples/paml/Technical/Simulation/multiruns.txt
- share/examples/paml/TipDate.FluH1/H1.Beast.Nulldata.xml
- share/examples/paml/TipDate.FluH1/H1.Beast.xml
- share/examples/paml/TipDate.FluH1/H1.NodeNumbers.tre
- share/examples/paml/TipDate.FluH1/H1.nexus
- share/examples/paml/TipDate.FluH1/H1.tre
- share/examples/paml/TipDate.FluH1/H1.txt
- share/examples/paml/TipDate.FluH1/baseml.ctl
- share/examples/paml/TipDate.FluH1/commands.txt
- share/examples/paml/TipDate.FluH1/in.BV.HKYG5
- share/examples/paml/TipDate.FluH1/mcmctreeClock1.ctl
- share/examples/paml/TipDate.FluH1/mcmctreeClock2.ctl
- share/examples/paml/TipDate.FluH1/mcmctreeClock3.ctl
- share/examples/paml/TipDate.HIV2/HIV2ge.tre
- share/examples/paml/TipDate.HIV2/HIV2ge.txt
- share/examples/paml/TipDate.HIV2/README.txt
- share/examples/paml/TipDate.HIV2/baseml.ctl
- share/examples/paml/TipDate.HIV2/in.BV.HKYG5
The first 100 are listed.
distinfo 1
| File | Size | SHA256 |
|---|---|---|
| abacus-gene-paml-v4.10.10_GH0.tar.gz | 3.835148e+06 | 173e8754ad78000371099a96910f2c72b03a7b7b13c717405dc23385ae2f2c0f |
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