physamp_1.0.2-1_i386.deb


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Description

physamp - sample sequence alignment according to its corresponding phylogenetic tree

Property Value
Distribution Ubuntu 17.10 (Artful Aardvark)
Repository Ubuntu Universe i386
Package name physamp
Package version 1.0.2
Package release 1
Package architecture i386
Package type deb
Installed size 766 B
Download size 311.80 KB
Official Mirror archive.ubuntu.com
The PhySamp package currently contains one program, bppalnoptim, which
samples a sequence alignment by removing sequences in order to maximize
the number of sites suitable for a given analysis. The program has three
running modes:
* Interactive: the user will be iteratively proposed a set of choices
for sequence removal, with their corresponding site gains. The
procedure stops when the user does not want to remove more sequences,
and the resulting filtered alignment is written.
* Automatic: the user enters an a priori criterion for stopping
the filtering procedure (for instance a minimum number of
sequences to keep).
* Diagnostic: this mode allows one to plot the trade-off curve, by showing
the site gain as a function of the number of removed sequences.

Alternatives

Package Version Architecture Repository
physamp_1.0.2-1_amd64.deb 1.0.2 amd64 Ubuntu Universe
physamp - - -

Requires

Name Value
libbpp-core3 -
libbpp-phyl11 -
libbpp-seq11 -
libc6 >= 2.4
libgcc1 >= 1:3.0
libstdc++6 >= 5.2

Download

Type URL
Binary Package physamp_1.0.2-1_i386.deb
Source Package physamp

Install Howto

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

Files

Path
/usr/bin/bppalnoptim
/usr/bin/bppphysamp
/usr/share/doc/physamp/changelog.Debian.gz
/usr/share/doc/physamp/copyright
/usr/share/doc/physamp/examples/LSU/LSU.dnd
/usr/share/doc/physamp/examples/LSU/LSU.phy.gz
/usr/share/doc/physamp/examples/LSU/PhySamp.bpp
/usr/share/doc/physamp/examples/PF01049/AlnOptimAuto.bpp
/usr/share/doc/physamp/examples/PF01049/AlnOptimFasttree.bpp
/usr/share/doc/physamp/examples/PF01049/AlnOptimFasttreeStop.bpp
/usr/share/doc/physamp/examples/PF01049/PF01049_fasttree.dnd.gz
/usr/share/doc/physamp/examples/PF01049/PF01049_full.txt.gz
/usr/share/doc/physamp/examples/PF01049/README
/usr/share/doc/physamp/examples/PF01049/diagnostic.R
/usr/share/doc/physamp/examples/PF01049/runFasttree.sh
/usr/share/info/physamp.info.gz
/usr/share/man/man1/bppalnoptim.1.gz

Changelog

2017-07-20 - Julien Dutheil <julien.dutheil@univ-montp2.fr>
physamp (1.0.2-1) unstable; urgency=medium
[ Andreas Tille ]
* New upstream version
Closes: #868919
* d/watch pointing to Github
* Fix homepage
* debhelper 10
* Adjust versioned Build-Depends
* Standards-Version: 4.0.0 (no changes needed)
[ Julien Y. Dutheil ]
* Updated from upstream.
2016-08-13 - Andreas Tille <tille@debian.org>
physamp (0.2.0-1) unstable; urgency=medium
* Initial release (Closes: #834208)

See Also

Package Description
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
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pia_3.103-4build1_i386.deb movie player for xawtv
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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
pictor-unload_2.38-0ubuntu1_all.deb tool for unloading and renaming pictures from flash media
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