phyml-3.3.20190909,1.txz


Advertisement

Description

phyml - Simple, fast, and accurate algorithm to estimate large phylogenies

Property Value
Distribution FreeBSD 11
Repository FreeBSD Ports Quarterly i386
Package filename phyml-3.3.20190909,1.txz
Package name phyml
Package version 3.3.20190909,1
Package release -
Package architecture i386
Package type txz
Category biology
Homepage https://github.com/stephaneguindon/phyml
License GPLv3
Maintainer ports@FreeBSD.org
Download size 1.34 MB
Installed size 2.30 MB
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: https://github.com/stephaneguindon/phyml
Options:
- DOCS: on
- EXAMPLES: on
- MPICH: off
- OPENMPI: off
===>   NOTICE:
The phyml port currently does not have a maintainer. As a result, it is
more likely to have unresolved issues, not be up-to-date, or even be removed in
the future. To volunteer to maintain this port, please create an issue at:
https://bugs.freebsd.org/bugzilla
More information about port maintainership is available at:
https://www.freebsd.org/doc/en/articles/contributing/ports-contributing.html#maintain-port

Alternatives

Package Version Architecture Repository
phyml-3.3.20190909,1.txz 3.3.20190909,1 amd64 FreeBSD Ports Quarterly
phyml-3.3.20190909_1,1.txz 3.3.20190909 i386 FreeBSD Ports Latest
phyml-3.3.20190909_1,1.txz 3.3.20190909 amd64 FreeBSD Ports Latest
phyml - - -

Download

Type URL
Mirror pkg.freebsd.org
Binary Package phyml-3.3.20190909,1.txz
Source Package biology/phyml

Install Howto

Install phyml txz package:

# pkg install phyml

See Also

Package Description
physcalc-2.4_1.txz Flexible calculator that behaves much like units(1)
physfs-3.0.2.txz Library to provide abstract access to various archives
pianobar-2019.02.14_1.txz Command-line Pandora online radio player
pic2fig-1.4_2.txz Pic format to fig format converter
picard-2.2.1.txz Next generation MusicBrainz Tagger
picard-plugins-2.0.20190917.txz Plugins for Picard tagger
pick-3.0.1.txz Tool for choosing one option from a set of choices with an interface
picmi-19.08.1.txz Single player logic-based puzzle game
pico-alpine-2.21.99999_1.txz [Al]PIne's message COmposition editor and Pilot file manager
picoc-2.1_2.txz Very small C interpreter for scripting
picocom-3.1.txz Dumb Terminal Emulator
picojson-1.3.0.txz Header file only JSON parser/serializer in C++
picosat-965.txz Satisfiability (SAT) solver for boolean variables
picosha2-1.0.0.23.txz C++ header-only SHA256 hash generator
picp-0.6.8.txz Driver for the Microchip Picstart Plus development programmer
Advertisement
Advertisement