| Port details on branch 2022Q2 |
- phyml Simple, fast, and accurate algorithm to estimate large phylogenies
- 3.3.20220408_1,1 biology
 =0      3.3.20220408_1,1Version 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
- Port Added: 2009-07-21 01:10:33
- Last Update: 2023-05-08 08:25:50
- Commit Hash: 8e2ec28
- License: GPLv3
- WWW:
- https://github.com/stephaneguindon/phyml
- Description:
- 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.
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- Manual pages:
- FreshPorts has no man page information for this port.
- pkg-plist: as obtained via:
make generate-plist - Dependency lines:
-
- To install the port:
- cd /usr/ports/biology/phyml/ && make install clean
- To add the package, run one of these commands:
- pkg install biology/phyml
- pkg install phyml
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.- PKGNAME: phyml
- Flavors: there is no flavor information for this port.
- distinfo:
- TIMESTAMP = 1662105216
SHA256 (stephaneguindon-phyml-v3.3.20220408_GH0.tar.gz) = 9cef375c0186e8a8d4db72ac02148707624c97174ffac244167a138ceb9f65bd
SIZE (stephaneguindon-phyml-v3.3.20220408_GH0.tar.gz) = 1803950
Packages (timestamps in pop-ups are UTC):
- Dependencies
- NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
- Build dependencies:
-
- pkgconf>=1.3.0_1 : devel/pkgconf
- autoconf>=2.71 : devel/autoconf
- automake>=1.16.5 : devel/automake
- libtoolize : devel/libtool
- There are no ports dependent upon this port
Configuration Options:- ===> The following configuration options are available for phyml-3.3.20220408_1,1:
DOCS=on: Build and/or install documentation
EXAMPLES=on: Build and/or install examples
====> MPI (Message Passing Interface) support: you can only select none or one of them
MPICH=off: Parallel processing support via MPICH 3
OPENMPI=off: Parallel processing support via Open MPI
===> Use 'make config' to modify these settings
- Options name:
- biology_phyml
- USES:
- autoreconf libtool pkgconfig
- FreshPorts was unable to extract/find any pkg message
- Master Sites:
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