fasttree_2.1.9-1_i386.deb


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Description

fasttree - phylogenetic trees from alignments of nucleotide or protein sequences

Property Value
Distribution Debian 9 (Stretch)
Repository Debian Main i386
Package filename fasttree_2.1.9-1_i386.deb
Package name fasttree
Package version 2.1.9
Package release 1
Package architecture i386
Package type deb
Category science
Homepage http://www.microbesonline.org/fasttree/
License -
Maintainer Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Download size 131.07 KB
Installed size 453.00 KB
FastTree infers approximately-maximum-likelihood phylogenetic trees from
alignments of nucleotide or protein sequences. It handles alignments
with up to a million of sequences in a reasonable amount of time and
memory. For large alignments, FastTree is 100-1,000 times faster than
PhyML 3.0 or RAxML 7.
FastTree is more accurate than PhyML 3 with default settings, and much
more accurate than the distance-matrix methods that are traditionally
used for large alignments. FastTree uses the Jukes-Cantor or generalized
time-reversible (GTR) models of nucleotide evolution and the JTT
(Jones-Taylor-Thornton 1992) model of amino acid evolution. To account
for the varying rates of evolution across sites, FastTree uses a single
rate for each site (the "CAT" approximation). To quickly estimate the
reliability of each split in the tree, FastTree computes local support
values with the Shimodaira-Hasegawa test (these are the same as PhyML 3's
"SH-like local supports").
This package contains a single threaded version (fasttree) and a
parallel version which uses OpenMP (fasttreMP).

Alternatives

Package Version Architecture Repository
fasttree_2.1.9-1_amd64.deb 2.1.9 amd64 Debian Main
fasttree - - -

Requires

Name Value
libc6 >= 2.7
libgomp1 >= 4.9

Download

Type URL
Mirror ftp.br.debian.org
Binary Package fasttree_2.1.9-1_i386.deb
Source Package fasttree

Install Howto

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

Files

Path
/usr/bin/fasttree
/usr/bin/fasttreeMP
/usr/share/doc/fasttree/changelog.Debian.gz
/usr/share/doc/fasttree/changelog.gz
/usr/share/doc/fasttree/copyright
/usr/share/man/man1/fasttree.1.gz
/usr/share/man/man1/fasttreeMP.1.gz

Changelog

2016-04-20 - Andreas Tille <tille@debian.org>
fasttree (2.1.9-1) unstable; urgency=medium
* New upstream version
* Use xz compression for source tarball
* cme fix dpkg-control
* Better hardening
2015-07-17 - Andreas Tille <tille@debian.org>
fasttree (2.1.8-2) unstable; urgency=medium
* Upload to unstable
2015-03-31 - Roland Fehrenbacher <rf@q-leap.de>
fasttree (2.1.8-1) experimental; urgency=medium
[ Andreas Tille ]
* Move debian/upstream to debian/upstream/metadata
* cme fix dpkg-control
* Priority: optional
* d/rules: cleanup from cruft
[ Roland Fehrenbacher ]
* New upstream version 2.1.8
* Makes debian/patches/increase-branch-length-precision.patch obsolete
2015-03-24 - Roland Fehrenbacher <rf@q-leap.de>
fasttree (2.1.7-2) unstable; urgency=low
* Team upload
* Modify/add patches to use double precision and increase branch
length precision. This is absolutely crucial to prevent flawed datas
analysis as described e.g. in
http://darlinglab.org/blog/2015/03/23/not-so-fast-fasttree.html
Closes: #781259
2014-02-25 - Tim Booth <tbooth@ceh.ac.uk>
fasttree (2.1.7-1biolinux1) precise; urgency=low
* Added upstream changelog into package and backport for
Bio-Linux.
* Fixed clean: target to remove both binaries.
2013-05-06 - Thorsten Alteholz <debian@alteholz.de>
fasttree (2.1.7-1) unstable; urgency=low
* New upstream version
* debian/control: remove DM-Upload-Allowed:
* debian/control: bump standards version to 3.9.4
2012-11-02 - Thorsten Alteholz <debian@alteholz.de>
fasttree (2.1.5-1) unstable; urgency=low
* New upstream version
2012-06-16 - Andreas Tille <tille@debian.org>
fasttree (2.1.4-2) UNRELEASED; urgency=low
* Fix name of upstream file and add eprint
2012-06-15 - Thorsten Alteholz <debian@alteholz.de>
fasttree (2.1.4-1) unstable; urgency=low
* Initial release (Closes: #677648)

See Also

Package Description
fastx-toolkit_0.0.14-3_i386.deb FASTQ/A short nucleotide reads pre-processing tools
fatattr_1.0.1-13_i386.deb Utility to control attributes on a FAT filesystem
fatcat_1.0.5-1_i386.deb FAT filesystem explore, extract, repair, and forensic tool
fatrace_0.12-1+b1_i386.deb report system wide file access events
fatresize_1.0.2-9_i386.deb FAT16/FAT32 filesystem resizer
fatsort_1.3.365-1+b1_i386.deb utility for sorting FAT directory structures
faucc_20160511-1+b1_i386.deb C compiler generating Intel code for 16bit/32bit CPUs
fauhdlc_20130704-1.1_i386.deb experimental VHDL compiler and interpreter
faust-common_0.9.95~repack1-2_all.deb functional programming language for realtime audio applications - common files
faust_0.9.95~repack1-2_i386.deb functional programming language for realtime audio applications
faustworks_0.5~repack0-3_i386.deb IDE for Faust dsp programming language
fb-music-high_0.1.2+nmu1_all.deb High quality, large music files for Frozen-Bubble
fbautostart_2.718281828-1+b2_i386.deb XDG compliant autostarting app for Fluxbox
fbb_7.07-2+b1_i386.deb Packet radio mailbox and utilities
fbcat_0.3-1+b1_i386.deb framebuffer grabber
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