phast_1.5+dfsg-1_amd64.deb


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Description

phast - phylogenetic analysis with space/time models

Property Value
Distribution Ubuntu 19.04 (Disco Dingo)
Repository Ubuntu Universe amd64
Package filename phast_1.5+dfsg-1_amd64.deb
Package name phast
Package version 1.5+dfsg
Package release 1
Package architecture amd64
Package type deb
Category universe/science
Homepage http://compgen.cshl.edu/phast/
License -
Maintainer Ubuntu Developers <ubuntu-devel-discuss@lists.ubuntu.com>
Download size 2.02 MB
Installed size 27.56 MB
PHAST is a software package for comparative and evolutionary genomics.
It consists of about half a dozen major programs, plus more than a dozen
utilities for manipulating sequence alignments, phylogenetic trees, and
genomic annotations. For the most part, PHAST focuses on two kinds of
applications: the identification of novel functional elements, including
protein-coding exons and evolutionarily conserved sequences; and
statistical phylogenetic modeling, including estimation of model
parameters, detection of signatures of selection, and reconstruction of
ancestral sequences.
PHAST does not support phylogeny reconstruction or sequence alignment,
and it is designed for use with DNA sequences only (see Comparison).

Alternatives

Package Version Architecture Repository
phast_1.5+dfsg-1_i386.deb 1.5+dfsg i386 Ubuntu Universe
phast - - -

Requires

Name Value
libc6 >= 2.23
liblapack.so.3 -
liblapack3 -
libpcre3 -

Download

Type URL
Mirror archive.ubuntu.com
Binary Package phast_1.5+dfsg-1_amd64.deb
Source Package phast

Install Howto

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

Files

Path
/usr/bin/all_dists
/usr/bin/base_evolve
/usr/bin/chooseLines
/usr/bin/clean_genes
/usr/bin/consEntropy
/usr/bin/convert_coords
/usr/bin/display_rate_matrix
/usr/bin/dless
/usr/bin/dlessP
/usr/bin/draw_tree
/usr/bin/eval_predictions
/usr/bin/exoniphy
/usr/bin/hmm_train
/usr/bin/hmm_tweak
/usr/bin/hmm_view
/usr/bin/indelFit
/usr/bin/indelHistory
/usr/bin/maf_parse
/usr/bin/makeHKY
/usr/bin/modFreqs
/usr/bin/msa_diff
/usr/bin/msa_split
/usr/bin/msa_view
/usr/bin/pbsDecode
/usr/bin/pbsEncode
/usr/bin/pbsScoreMatrix
/usr/bin/pbsTrain
/usr/bin/phast
/usr/bin/phastBias
/usr/bin/phastCons
/usr/bin/phastMotif
/usr/bin/phastOdds
/usr/bin/phyloBoot
/usr/bin/phyloFit
/usr/bin/phyloP
/usr/bin/prequel
/usr/bin/refeature
/usr/bin/stringiphy
/usr/bin/treeGen
/usr/bin/tree_doctor
/usr/share/doc/phast/changelog.Debian.gz
/usr/share/doc/phast/copyright
/usr/share/man/man1/all_dists.1.gz
/usr/share/man/man1/base_evolve.1.gz
/usr/share/man/man1/chooseLines.1.gz
/usr/share/man/man1/clean_genes.1.gz
/usr/share/man/man1/consEntropy.1.gz
/usr/share/man/man1/convert_coords.1.gz
/usr/share/man/man1/display_rate_matrix.1.gz
/usr/share/man/man1/dless.1.gz
/usr/share/man/man1/dlessP.1.gz
/usr/share/man/man1/draw_tree.1.gz
/usr/share/man/man1/eval_predictions.1.gz
/usr/share/man/man1/exoniphy.1.gz
/usr/share/man/man1/hmm_train.1.gz
/usr/share/man/man1/hmm_tweak.1.gz
/usr/share/man/man1/hmm_view.1.gz
/usr/share/man/man1/indelFit.1.gz
/usr/share/man/man1/indelHistory.1.gz
/usr/share/man/man1/maf_parse.1.gz
/usr/share/man/man1/makeHKY.1.gz
/usr/share/man/man1/modFreqs.1.gz
/usr/share/man/man1/msa_diff.1.gz
/usr/share/man/man1/msa_split.1.gz
/usr/share/man/man1/msa_view.1.gz
/usr/share/man/man1/pbsDecode.1.gz
/usr/share/man/man1/pbsEncode.1.gz
/usr/share/man/man1/pbsScoreMatrix.1.gz
/usr/share/man/man1/pbsTrain.1.gz
/usr/share/man/man1/phast.1.gz
/usr/share/man/man1/phastBias.1.gz
/usr/share/man/man1/phastCons.1.gz
/usr/share/man/man1/phastMotif.1.gz
/usr/share/man/man1/phastOdds.1.gz
/usr/share/man/man1/phyloBoot.1.gz
/usr/share/man/man1/phyloFit.1.gz
/usr/share/man/man1/phyloP.1.gz
/usr/share/man/man1/prequel.1.gz
/usr/share/man/man1/refeature.1.gz
/usr/share/man/man1/stringiphy.1.gz
/usr/share/man/man1/treeGen.1.gz
/usr/share/man/man1/tree_doctor.1.gz
/usr/share/phast/data/exoniphy/default-no-cns.cm
/usr/share/phast/data/exoniphy/default.cm
/usr/share/phast/data/exoniphy/models
/usr/share/phast/data/exoniphy/models-gc1
/usr/share/phast/data/exoniphy/models-gc2
/usr/share/phast/data/exoniphy/models-gc3
/usr/share/phast/data/exoniphy/models-gc4
/usr/share/phast/data/exoniphy/models-gc5
/usr/share/phast/data/exoniphy/models-no-cns
/usr/share/phast/data/exoniphy/models-no-cns-gc1
/usr/share/phast/data/exoniphy/models-no-cns-gc2
/usr/share/phast/data/exoniphy/models-no-cns-gc3
/usr/share/phast/data/exoniphy/models-no-cns-gc4
/usr/share/phast/data/exoniphy/models-no-cns-gc5
/usr/share/phast/data/exoniphy/mammals/cftr25_hybrid.nh
/usr/share/phast/data/exoniphy/mammals/default-indels-no-cns.hmm
/usr/share/phast/data/exoniphy/mammals/default-indels.hmm
/usr/share/phast/data/exoniphy/mammals/default-no-cns.hmm
/usr/share/phast/data/exoniphy/mammals/default.hmm
/usr/share/phast/data/exoniphy/mammals/hky.3'splice-1.mod
/usr/share/phast/data/exoniphy/mammals/hky.3'splice-2.mod
/usr/share/phast/data/exoniphy/mammals/hky.3'splice-3.mod
/usr/share/phast/data/exoniphy/mammals/hky.3'splice-4.mod
/usr/share/phast/data/exoniphy/mammals/hky.3'splice-5.mod
/usr/share/phast/data/exoniphy/mammals/hky.3'splice-6.mod
/usr/share/phast/data/exoniphy/mammals/hky.5'splice-1.mod
/usr/share/phast/data/exoniphy/mammals/hky.5'splice-2.mod
/usr/share/phast/data/exoniphy/mammals/hky.5'splice-3.mod
/usr/share/phast/data/exoniphy/mammals/hky.5'splice-4.mod
/usr/share/phast/data/exoniphy/mammals/hky.5'splice-5.mod
/usr/share/phast/data/exoniphy/mammals/hky.5'splice-6.mod
/usr/share/phast/data/exoniphy/mammals/hky.cds3'ss.mod
/usr/share/phast/data/exoniphy/mammals/hky.cds5'ss-1.mod
/usr/share/phast/data/exoniphy/mammals/hky.cds5'ss-2.mod
/usr/share/phast/data/exoniphy/mammals/hky.cds5'ss-3.mod
/usr/share/phast/data/exoniphy/mammals/hky.prestart-1.mod
/usr/share/phast/data/exoniphy/mammals/hky.prestart-2.mod
/usr/share/phast/data/exoniphy/mammals/hky.prestart-3.mod
/usr/share/phast/data/exoniphy/mammals/hky.prestart-4.mod
/usr/share/phast/data/exoniphy/mammals/hky.start-1.mod
/usr/share/phast/data/exoniphy/mammals/hky.start-2.mod
/usr/share/phast/data/exoniphy/mammals/hky.start-3.mod
/usr/share/phast/data/exoniphy/mammals/hky.stop-1.mod
/usr/share/phast/data/exoniphy/mammals/hky.stop-2.mod
/usr/share/phast/data/exoniphy/mammals/hky.stop-3.mod
/usr/share/phast/data/exoniphy/mammals/r3.cds-1.gc1.mod
/usr/share/phast/data/exoniphy/mammals/r3.cds-1.gc2.mod
/usr/share/phast/data/exoniphy/mammals/r3.cds-1.gc3.mod
/usr/share/phast/data/exoniphy/mammals/r3.cds-1.gc4.mod
/usr/share/phast/data/exoniphy/mammals/r3.cds-1.gc5.mod
/usr/share/phast/data/exoniphy/mammals/r3.cds-1.mod
/usr/share/phast/data/exoniphy/mammals/r3.cds-2.gc1.mod
/usr/share/phast/data/exoniphy/mammals/r3.cds-2.gc2.mod
/usr/share/phast/data/exoniphy/mammals/r3.cds-2.gc3.mod
/usr/share/phast/data/exoniphy/mammals/r3.cds-2.gc4.mod
/usr/share/phast/data/exoniphy/mammals/r3.cds-2.gc5.mod
/usr/share/phast/data/exoniphy/mammals/r3.cds-2.mod
/usr/share/phast/data/exoniphy/mammals/r3.cds-3.gc1.mod
/usr/share/phast/data/exoniphy/mammals/r3.cds-3.gc2.mod
/usr/share/phast/data/exoniphy/mammals/r3.cds-3.gc3.mod
/usr/share/phast/data/exoniphy/mammals/r3.cds-3.gc4.mod
/usr/share/phast/data/exoniphy/mammals/r3.cds-3.gc5.mod
/usr/share/phast/data/exoniphy/mammals/r3.cds-3.mod
/usr/share/phast/data/exoniphy/mammals/r3.cns.gc1.mod
/usr/share/phast/data/exoniphy/mammals/r3.cns.gc2.mod
/usr/share/phast/data/exoniphy/mammals/r3.cns.gc3.mod
/usr/share/phast/data/exoniphy/mammals/r3.cns.gc4.mod
/usr/share/phast/data/exoniphy/mammals/r3.cns.gc5.mod
/usr/share/phast/data/exoniphy/mammals/r3.cns.mod
/usr/share/phast/data/exoniphy/mammals/r3.ncns.gc1.mod
/usr/share/phast/data/exoniphy/mammals/r3.ncns.gc2.mod
/usr/share/phast/data/exoniphy/mammals/r3.ncns.gc3.mod
/usr/share/phast/data/exoniphy/mammals/r3.ncns.gc4.mod
/usr/share/phast/data/exoniphy/mammals/r3.ncns.gc5.mod
/usr/share/phast/data/exoniphy/mammals/r3.ncns.mod
/usr/share/phast/data/exoniphy/mammals/r3.noncoding.gc1.mod
/usr/share/phast/data/exoniphy/mammals/r3.noncoding.gc2.mod
/usr/share/phast/data/exoniphy/mammals/r3.noncoding.gc3.mod
/usr/share/phast/data/exoniphy/mammals/r3.noncoding.gc4.mod
/usr/share/phast/data/exoniphy/mammals/r3.noncoding.gc5.mod
/usr/share/phast/data/exoniphy/mammals/r3.noncoding.mod
/usr/share/phast/data/phastCons/simple-coding-indels.hmm
/usr/share/phast/data/phastCons/simple-coding.hmm

Changelog

2018-10-19 - Andreas Tille <tille@debian.org>
phast (1.5+dfsg-1) unstable; urgency=medium
* New upstream version
* Fix homepage
* debhelper 11
* Point Vcs fields to salsa.debian.org
* Standards-Version: 4.2.1
* Run part or the test suite
2017-09-12 - Andreas Tille <tille@debian.org>
phast (1.4+dfsg-1) unstable; urgency=medium
* Initial release (Closes: #875555)

See Also

Package Description
phenny_2~hg28-3_all.deb extensible IRC bot written in Python
phing_2.16.1-1_all.deb PHP5 project build system based on Apache Ant
phipack_0.0.20160614-3_amd64.deb PHI test and other tests of recombination
phlipple-data_0.8.5-4build1_all.deb reduce 3D shapes to a single square - game data
phlipple_0.8.5-4build1_amd64.deb reduce 3D shapes to a single square
phnxdeco_0.33-3build1_amd64.deb Decompress flashfiles equipped with a PHOENIX BIOS
phonon-backend-gstreamer-common_4.9.0-1_amd64.deb Phonon GStreamer 1.0.x backend icons
phonon-backend-gstreamer_4.9.0-1_amd64.deb Phonon GStreamer 1.0 backend
phonon-backend-null_4.10.2-1_amd64.deb multimedia framework from KDE - null back-end (no real back-end)
phonon-backend-vlc_0.10.2-1_amd64.deb Phonon VLC backend
phonon4qt5-backend-gstreamer_4.9.0-1_amd64.deb Phonon Qt5 GStreamer 1.0 backend
phonon4qt5-backend-null_4.10.2-1_amd64.deb multimedia framework from KDE using Qt 5 - null back-end (no real back-end)
phonon4qt5-backend-vlc_0.10.2-1_amd64.deb Phonon4Qt5 VLC backend
phonon4qt5_4.10.2-1_amd64.deb multimedia framework from KDE using Qt 5 - metapackage
phonon_4.10.2-1_amd64.deb multimedia framework from KDE using Qt 4 - metapackage
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