phyml_3.3.20170530+dfsg-2_i386.deb


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Description

phyml - Phylogenetic estimation using Maximum Likelihood

Property Value
Distribution Ubuntu 17.10 (Artful Aardvark)
Repository Ubuntu Universe i386
Package name phyml
Package version 3.3.20170530+dfsg
Package release 2
Package architecture i386
Package type deb
Installed size 5.10 KB
Download size 1.43 MB
Official Mirror archive.ubuntu.com
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
be 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.
This package also includes PhyTime.

Alternatives

Package Version Architecture Repository
phyml_3.3.20170530+dfsg-2_amd64.deb 3.3.20170530+dfsg amd64 Ubuntu Universe
phyml - - -

Requires

Name Value
libc6 >= 2.7
libopenmpi2 -
openmpi-bin -

Download

Type URL
Binary Package phyml_3.3.20170530+dfsg-2_i386.deb
Source Package phyml

Install Howto

  1. Update the package index:
    # sudo apt-get update
  2. Install phyml deb package:
    # sudo apt-get install phyml

Files

Path
/usr/bin/phyml
/usr/bin/phyml-mpi
/usr/lib/phyml/bin/phyml
/usr/lib/phyml/bin/phyml-mpi
/usr/share/doc-base/phyml
/usr/share/doc/phyml/README.Debian
/usr/share/doc/phyml/changelog.Debian.gz
/usr/share/doc/phyml/copyright
/usr/share/doc/phyml/phyml_manual.pdf
/usr/share/doc/phyml/examples/example.nex.gz
/usr/share/doc/phyml/examples/nexus_example.nxs
/usr/share/doc/phyml/examples/nucleic.gz
/usr/share/doc/phyml/examples/proteic.gz
/usr/share/doc/phyml/examples/lg4x/X1.mat
/usr/share/doc/phyml/examples/lg4x/X2.mat
/usr/share/doc/phyml/examples/lg4x/X3.mat
/usr/share/doc/phyml/examples/lg4x/X4.mat
/usr/share/doc/phyml/examples/lg4x/lg4x.xml
/usr/share/doc/phyml/examples/phyrex_input_files/h1n1.nxs.gz
/usr/share/doc/phyml/examples/phyrex_input_files/usa_coord.txt
/usr/share/doc/phyml/examples/phytime_input_files/p1.calib
/usr/share/doc/phyml/examples/phytime_input_files/p1.nxs.gz
/usr/share/doc/phyml/examples/phytime_input_files/p1.tree
/usr/share/man/man1/phyml.1.gz

Changelog

2017-06-30 - Graham Inggs <ginggs@debian.org>
phyml (3:3.3.20170530+dfsg-2) unstable; urgency=medium
* Team upload
* Do not emit -march=native (Closes: #866139)
* Drop autopkgtest dependency on pocl-opencl-icd
2017-06-27 - Andreas Tille <tille@debian.org>
phyml (3:3.3.20170530+dfsg-1) unstable; urgency=medium
* New upstream version
* Upstream confirmed that beagle is not supported
* Standards-Version: 4.0.0 (no changes needed)
* Do not disable PIE
Closes: #865654
* Do not build phytime since it is not supported any more
2017-02-01 - Andreas Tille <tille@debian.org>
phyml (3:3.2.0+dfsg-7) unstable; urgency=medium
* Fix bug in wrapper script which really
Closes: #853738
2017-01-31 - Andreas Tille <tille@debian.org>
phyml (3:3.2.0+dfsg-6) unstable; urgency=medium
* Also provide version without beagle library since it causes trouble
on machines without according graphics hardware
Closes: #853737
* Provide link /usr/bin/phyml-beagle
* Enable to switch of MPI version via environment variable since there
are circumstances when it leads to wrong results
Closes: #853738
* Test single processor and MPI in autopkgtest
2017-01-30 - Andreas Tille <tille@debian.org>
phyml (3:3.2.0+dfsg-5) unstable; urgency=medium
* Fix wrapper to correctly use mpirun
Closes: #853211
2017-01-16 - Andreas Tille <tille@debian.org>
phyml (3:3.2.0+dfsg-4) unstable; urgency=medium
* Add pocl-opencl-icd to autopkgtest dependencies to emulate CPU-based ICD
* debhelper 10
* d/watch: version=4
* Use chrpath to remove RPATH from binary
* Use "OMPI_MCA_plm_rsh_agent=/bin/false" in test (see #494046)
2016-10-12 - Canberk Koç	 <canberkkoc@gmail.com>
phyml (3:3.2.0+dfsg-3) unstable; urgency=medium
* Team upload
[ Canberk Koç ]
* autopkgtest added
* fix autopkgtest 
[ Andreas Tille ]
* Add missing Depends: openmpi-bin
* use wrapper to select MPI version if applicable
* Use compression options in d/watch
* Fix missing declaration
* hardening=+all,-pie
2016-03-14 - Andreas Tille <tille@debian.org>
phyml (3:3.2.0+dfsg-2) unstable; urgency=medium
[ Kevin Murray ]
* Fix VCS link in d/control
* Patch for reproduible build (configure.ac date)
* Bump standards version to 3.9.7
[ Andreas Tille ]
* Enable MPI version of phyml
2016-02-06 - Kevin Murray <spam@kdmurray.id.au>
phyml (3:3.2.0+dfsg-1) unstable; urgency=medium
[ Kevin Murray ]
* New upstream release
* d/watch: Source has changed location on Github
* Patch CPPFLAGS to allow build of phytime
[ Andreas Tille ]
* Upstream confirmed that the development version should be fairly stable
and most probably suitable for Debian
* Moved debian/upstream to debian/upstream/metadata
* cme fix dpkg-control
* Remove executable binary from archive (as well as LaTeX remainings once
we are starting to remove files)
* Move to git
* Build-Depends: pkg-config, libhmsbeagle-dev
* debian/rules:
- hack around removal of PDF manual
- enable building with libhmsbeagle-dev
* DEP5
2013-08-05 - Andreas Tille <tille@debian.org>
phyml (2:20120412-2) unstable; urgency=low
* debian/patches/sse_only_if_supported.patch: Check architecture before
deciding to build using -msse
Closes: #718747

See Also

Package Description
physamp_1.0.2-1_i386.deb sample sequence alignment according to its corresponding phylogenetic tree
physlock_11-1_i386.deb lightweight Linux console locking tool
phyutility_2.7.3-1_i386.deb simple analyses or modifications on both phylogenetic trees and data matrices
pi_1.3.4-2_i386.deb Compute Archimedes' constant Pi to arbitrary precision
pia_3.103-4build1_i386.deb movie player for xawtv
pianobar_2017.08.30-1_i386.deb console based player for Pandora radio
pianobooster_0.6.7~svn156-1_i386.deb learn the piano just by playing a game
picard-tools_2.8.1+dfsg-2_all.deb Command line tools to manipulate SAM and BAM files
picard_1.4.2-1_i386.deb Next-Generation MusicBrainz audio files tagger
pick_1.8.0-1_i386.deb utility to choose one option from a set of choices
picmi_17.04.3-0ubuntu1_i386.deb Number logic game
picocom_2.2-2_i386.deb minimal dumb-terminal emulation program
picolisp_17.6-1_i386.deb Lisp interpreter and application server framework
picosat_960-1_i386.deb SAT solver with proof and core support
picprog_1.9.1-3_i386.deb Microchip PIC serial programmer software
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