altree-examples_1.3.1-2_all.deb


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Description

altree-examples - example files for ALTree

Property Value
Distribution Debian 8 (Jessie)
Repository Debian Main amd64
Package name altree-examples
Package version 1.3.1
Package release 2
Package architecture all
Package type deb
Installed size 614 B
Download size 323.23 KB
Official Mirror ftp.br.debian.org
ALTree was designed to perform association detection and localization of
susceptibility sites using haplotype phylogenetic trees: first, it allows the
detection of an association between a candidate gene and a disease, and second,
it enables to make hypothesis about the susceptibility loci.
This package contains the example files for the ALTree package discussed in
its PDF manual.

Alternatives

Package Version Architecture Repository
altree-examples_1.3.1-2_all.deb 1.3.1 all Debian Main
altree-examples - - -

Download

Type URL
Binary Package altree-examples_1.3.1-2_all.deb
Source Package altree

Install Howto

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

Files

Path
/usr/share/doc/altree-examples/changelog.Debian.gz
/usr/share/doc/altree-examples/changelog.gz
/usr/share/doc/altree-examples/copyright
/usr/share/doc/altree-examples/create_file/paup_file/caco.phase.gz
/usr/share/doc/altree-examples/create_file/paup_file/caco.phase.out.gz
/usr/share/doc/altree-examples/create_file/paup_file/caco.phase.out_freqs
/usr/share/doc/altree-examples/create_file/paup_file/caco.phase.out_monitor
/usr/share/doc/altree-examples/create_file/paup_file/caco.phase.out_pairs.gz
/usr/share/doc/altree-examples/create_file/paup_file/caco.phase.out_recom.gz
/usr/share/doc/altree-examples/create_file/paup_file/caco.prepaup
/usr/share/doc/altree-examples/create_file/paup_file/create_file
/usr/share/doc/altree-examples/create_file/paup_file/nb_cas_control.txt
/usr/share/doc/altree-examples/create_file/phy-paml_file/NUM
/usr/share/doc/altree-examples/create_file/phy-paml_file/create_file
/usr/share/doc/altree-examples/create_file/phy-paml_file/fam19_0.gm
/usr/share/doc/altree-examples/create_file/phy-paml_file/fam19_0.gz
/usr/share/doc/altree-examples/create_file/phy-paml_file/fam19_0_H1_HAPLOTYPES.gz
/usr/share/doc/altree-examples/create_file/phy-paml_file/fam19_0_LDmeasuresCASES.xt
/usr/share/doc/altree-examples/create_file/phy-paml_file/fam19_0_LDmeasuresCONTROLS.xt
/usr/share/doc/altree-examples/create_file/phy-paml_file/nb_cas_control.txt
/usr/share/doc/altree-examples/create_file/phy-paml_file/trio.fmh.gz
/usr/share/doc/altree-examples/create_file/phy-paml_file/trio.phy
/usr/share/doc/altree-examples/create_file/phy-paml_file/trio.prephy
/usr/share/doc/altree-examples/paml/tree_building_using_phyML/run_phyML
/usr/share/doc/altree-examples/paml/tree_building_using_phyML/trio2.phy
/usr/share/doc/altree-examples/paml/tree_building_using_phyML/trio2.phy_phyml_lk.txt
/usr/share/doc/altree-examples/paml/tree_building_using_phyML/trio2.phy_phyml_stat.txt
/usr/share/doc/altree-examples/paml/tree_building_using_phyML/trio2.phy_phyml_tree.txt
/usr/share/doc/altree-examples/paml/unrooted_absent/association/1_trio_ML.asso.gz
/usr/share/doc/altree-examples/paml/unrooted_absent/association/2base.t.gz
/usr/share/doc/altree-examples/paml/unrooted_absent/association/baseml.ctl
/usr/share/doc/altree-examples/paml/unrooted_absent/association/lnf
/usr/share/doc/altree-examples/paml/unrooted_absent/association/mlb.gz
/usr/share/doc/altree-examples/paml/unrooted_absent/association/nb_cas_control.txt
/usr/share/doc/altree-examples/paml/unrooted_absent/association/rst.gz
/usr/share/doc/altree-examples/paml/unrooted_absent/association/rst1
/usr/share/doc/altree-examples/paml/unrooted_absent/association/rub.gz
/usr/share/doc/altree-examples/paml/unrooted_absent/association/run_altree
/usr/share/doc/altree-examples/paml/unrooted_absent/association/trio2.phy
/usr/share/doc/altree-examples/paml/unrooted_absent/association/trio2.phy_phyml_tree.txt
/usr/share/doc/altree-examples/paml/unrooted_present/association/1_trio_ML.asso.gz
/usr/share/doc/altree-examples/paml/unrooted_present/association/2base.t.gz
/usr/share/doc/altree-examples/paml/unrooted_present/association/baseml.ctl
/usr/share/doc/altree-examples/paml/unrooted_present/association/lnf
/usr/share/doc/altree-examples/paml/unrooted_present/association/mlb.gz
/usr/share/doc/altree-examples/paml/unrooted_present/association/nb_cas_control.txt
/usr/share/doc/altree-examples/paml/unrooted_present/association/rst.gz
/usr/share/doc/altree-examples/paml/unrooted_present/association/rst1
/usr/share/doc/altree-examples/paml/unrooted_present/association/rub.gz
/usr/share/doc/altree-examples/paml/unrooted_present/association/run_altree
/usr/share/doc/altree-examples/paml/unrooted_present/association/trio2.phy
/usr/share/doc/altree-examples/paml/unrooted_present/association/trio2.phy_phyml_tree.txt
/usr/share/doc/altree-examples/paml/unrooted_present/localisation/2base.t.gz
/usr/share/doc/altree-examples/paml/unrooted_present/localisation/baseml.ctl
/usr/share/doc/altree-examples/paml/unrooted_present/localisation/et_trio2.phy
/usr/share/doc/altree-examples/paml/unrooted_present/localisation/lnf
/usr/share/doc/altree-examples/paml/unrooted_present/localisation/mlb.gz
/usr/share/doc/altree-examples/paml/unrooted_present/localisation/nb_cas_controls.txt
/usr/share/doc/altree-examples/paml/unrooted_present/localisation/rst.gz
/usr/share/doc/altree-examples/paml/unrooted_present/localisation/rst1
/usr/share/doc/altree-examples/paml/unrooted_present/localisation/rub.gz
/usr/share/doc/altree-examples/paml/unrooted_present/localisation/run-prog
/usr/share/doc/altree-examples/paml/unrooted_present/localisation/trio2.loc
/usr/share/doc/altree-examples/paml/unrooted_present/localisation/trio2.phy
/usr/share/doc/altree-examples/paml/unrooted_present/localisation/trio2.phy_phyml_tree.txt
/usr/share/doc/altree-examples/paup/ancestor_absent/association/1_caco.asso
/usr/share/doc/altree-examples/paup/ancestor_absent/association/caco.paup
/usr/share/doc/altree-examples/paup/ancestor_absent/association/nb_cas_control.txt
/usr/share/doc/altree-examples/paup/ancestor_absent/association/run_altree
/usr/share/doc/altree-examples/paup/ancestor_absent/association/test.res.log.gz
/usr/share/doc/altree-examples/paup/ancestor_absent/association/test.tree.gz
/usr/share/doc/altree-examples/paup/ancestor_absent/localisation/caco.loc
/usr/share/doc/altree-examples/paup/ancestor_absent/localisation/caco.paup
/usr/share/doc/altree-examples/paup/ancestor_absent/localisation/et_caco.paup
/usr/share/doc/altree-examples/paup/ancestor_absent/localisation/nb_cas_control.txt
/usr/share/doc/altree-examples/paup/ancestor_absent/localisation/run-prog
/usr/share/doc/altree-examples/paup/ancestor_absent/localisation/test.res.log.gz
/usr/share/doc/altree-examples/paup/ancestor_absent/localisation/test.tree.gz
/usr/share/doc/altree-examples/paup/ancestor_present/association/1_caco.asso
/usr/share/doc/altree-examples/paup/ancestor_present/association/caco.paup
/usr/share/doc/altree-examples/paup/ancestor_present/association/nb_cas_control.txt
/usr/share/doc/altree-examples/paup/ancestor_present/association/run_altree
/usr/share/doc/altree-examples/paup/ancestor_present/association/test.res.log
/usr/share/doc/altree-examples/paup/ancestor_present/association/test.tree.gz
/usr/share/doc/altree-examples/paup/ancestor_present/localisation/caco.loc
/usr/share/doc/altree-examples/paup/ancestor_present/localisation/caco.paup
/usr/share/doc/altree-examples/paup/ancestor_present/localisation/et_caco.paup
/usr/share/doc/altree-examples/paup/ancestor_present/localisation/nb_cas_control.txt
/usr/share/doc/altree-examples/paup/ancestor_present/localisation/run-prog
/usr/share/doc/altree-examples/paup/ancestor_present/localisation/test.res.log.gz
/usr/share/doc/altree-examples/paup/ancestor_present/localisation/test.tree.gz
/usr/share/doc/altree-examples/paup/outgr_absent/association/1_caco.asso
/usr/share/doc/altree-examples/paup/outgr_absent/association/caco.paup
/usr/share/doc/altree-examples/paup/outgr_absent/association/nb_cas_control.txt
/usr/share/doc/altree-examples/paup/outgr_absent/association/run_altree
/usr/share/doc/altree-examples/paup/outgr_absent/association/test.res.log.gz
/usr/share/doc/altree-examples/paup/outgr_absent/association/test.tree.gz
/usr/share/doc/altree-examples/paup/outgr_absent/localisation/caco.loc
/usr/share/doc/altree-examples/paup/outgr_absent/localisation/caco.paup
/usr/share/doc/altree-examples/paup/outgr_absent/localisation/et_caco.paup
/usr/share/doc/altree-examples/paup/outgr_absent/localisation/nb_cas_control.txt
/usr/share/doc/altree-examples/paup/outgr_absent/localisation/run-prog
/usr/share/doc/altree-examples/paup/outgr_absent/localisation/test.res.log.gz
/usr/share/doc/altree-examples/paup/outgr_absent/localisation/test.tree.gz
/usr/share/doc/altree-examples/paup/outgr_present/association/1_caco.asso
/usr/share/doc/altree-examples/paup/outgr_present/association/caco.paup
/usr/share/doc/altree-examples/paup/outgr_present/association/nb_cas_control.txt
/usr/share/doc/altree-examples/paup/outgr_present/association/run_altree
/usr/share/doc/altree-examples/paup/outgr_present/association/test.res.log.gz
/usr/share/doc/altree-examples/paup/outgr_present/association/test.tree.gz
/usr/share/doc/altree-examples/paup/outgr_present/localisation/caco.loc
/usr/share/doc/altree-examples/paup/outgr_present/localisation/caco.paup
/usr/share/doc/altree-examples/paup/outgr_present/localisation/et_caco.paup
/usr/share/doc/altree-examples/paup/outgr_present/localisation/nb_cas_control.txt
/usr/share/doc/altree-examples/paup/outgr_present/localisation/run-prog
/usr/share/doc/altree-examples/paup/outgr_present/localisation/test.res.log.gz
/usr/share/doc/altree-examples/paup/outgr_present/localisation/test.tree.gz
/usr/share/doc/altree-examples/paup/unrooted_absent/association/1_caco.asso
/usr/share/doc/altree-examples/paup/unrooted_absent/association/caco.paup
/usr/share/doc/altree-examples/paup/unrooted_absent/association/nb_cas_control.txt
/usr/share/doc/altree-examples/paup/unrooted_absent/association/run_altree
/usr/share/doc/altree-examples/paup/unrooted_absent/association/test.res.log.gz
/usr/share/doc/altree-examples/paup/unrooted_absent/association/test.tree.gz
/usr/share/doc/altree-examples/paup/unrooted_absent/localisation/caco.loc
/usr/share/doc/altree-examples/paup/unrooted_absent/localisation/caco.paup
/usr/share/doc/altree-examples/paup/unrooted_absent/localisation/et_caco.paup
/usr/share/doc/altree-examples/paup/unrooted_absent/localisation/nb_cas_control.txt
/usr/share/doc/altree-examples/paup/unrooted_absent/localisation/run-prog
/usr/share/doc/altree-examples/paup/unrooted_absent/localisation/test.res.log.gz
/usr/share/doc/altree-examples/paup/unrooted_absent/localisation/test.tree.gz
/usr/share/doc/altree-examples/paup/unrooted_present/association/1_caco.asso
/usr/share/doc/altree-examples/paup/unrooted_present/association/caco.paup
/usr/share/doc/altree-examples/paup/unrooted_present/association/nb_cas_control.txt
/usr/share/doc/altree-examples/paup/unrooted_present/association/run_altree
/usr/share/doc/altree-examples/paup/unrooted_present/association/test.res.log.gz
/usr/share/doc/altree-examples/paup/unrooted_present/association/test.tree.gz
/usr/share/doc/altree-examples/paup/unrooted_present/localisation/caco.loc
/usr/share/doc/altree-examples/paup/unrooted_present/localisation/caco.paup
/usr/share/doc/altree-examples/paup/unrooted_present/localisation/et_caco.paup
/usr/share/doc/altree-examples/paup/unrooted_present/localisation/nb_cas_control.txt
/usr/share/doc/altree-examples/paup/unrooted_present/localisation/run-prog
/usr/share/doc/altree-examples/paup/unrooted_present/localisation/test.res.log.gz
/usr/share/doc/altree-examples/paup/unrooted_present/localisation/test.tree.gz
/usr/share/doc/altree-examples/phylip/ancestor_absent/association/1_trio_phy.asso.gz
/usr/share/doc/altree-examples/phylip/ancestor_absent/association/ancestors
/usr/share/doc/altree-examples/phylip/ancestor_absent/association/nb_cas_controls.txt
/usr/share/doc/altree-examples/phylip/ancestor_absent/association/outfile.gz
/usr/share/doc/altree-examples/phylip/ancestor_absent/association/outtree.gz
/usr/share/doc/altree-examples/phylip/ancestor_absent/association/run_altree
/usr/share/doc/altree-examples/phylip/ancestor_absent/association/trio.phy
/usr/share/doc/altree-examples/phylip/ancestor_present/association/1_trio_phy.asso.gz
/usr/share/doc/altree-examples/phylip/ancestor_present/association/ancestors
/usr/share/doc/altree-examples/phylip/ancestor_present/association/nb_cas_controls.txt
/usr/share/doc/altree-examples/phylip/ancestor_present/association/outfile.gz
/usr/share/doc/altree-examples/phylip/ancestor_present/association/outtree.gz
/usr/share/doc/altree-examples/phylip/ancestor_present/association/run_altree
/usr/share/doc/altree-examples/phylip/ancestor_present/association/trio.phy
/usr/share/doc/altree-examples/phylip/outgroup_absent/association/1_trio_phy.asso.gz
/usr/share/doc/altree-examples/phylip/outgroup_absent/association/nb_cas_controls.txt
/usr/share/doc/altree-examples/phylip/outgroup_absent/association/outfile.gz
/usr/share/doc/altree-examples/phylip/outgroup_absent/association/outtree.gz
/usr/share/doc/altree-examples/phylip/outgroup_absent/association/run_altree
/usr/share/doc/altree-examples/phylip/outgroup_absent/association/trio.phy
/usr/share/doc/altree-examples/phylip/outgroup_present/association/1_trio_phy.asso.gz
/usr/share/doc/altree-examples/phylip/outgroup_present/association/nb_cas_controls.txt
/usr/share/doc/altree-examples/phylip/outgroup_present/association/outfile.gz
/usr/share/doc/altree-examples/phylip/outgroup_present/association/outtree.gz
/usr/share/doc/altree-examples/phylip/outgroup_present/association/run_altree
/usr/share/doc/altree-examples/phylip/outgroup_present/association/trio.phy

Changelog

2014-03-30 - Vincent Danjean <vdanjean@debian.org>
altree (1.3.1-2) unstable; urgency=medium
* Fix "FTBFS with clang instead of gcc" 
clang does not support nested functions so removing them.
Instead of inlining the nested function as proposed in the submitted
patch (thanks Arthur <arthur@info9.net>), use a external function
with an explicit context (Closes: #742843)
* bump standard-version (no change needed)
2013-12-13 - Vincent Danjean <vdanjean@debian.org>
altree (1.3.1-1) unstable; urgency=low
* New upstream release
+ fix a SEGV when ALTREE_PARALLEL is used with more processors
than requested permutations (-r program parameter)
+ Fix "FTBFS with perl 5.12.0-1: long doubles" (Closes: #578550)
* debian/control:
Add B-D on libtest-deep-perl (required when fixing 578550)
2013-11-22 - Vincent Danjean <vdanjean@debian.org>
altree (1.3.0-1) unstable; urgency=low
* New upstream release
+ Mostly performance improvment
* debian/control:
+ bump Standard-Version (no change needed)
+ put canonical vcs fields
+ remove outdated DM-Upload-Allowed field
+ improve altree-examples long description
+ add libgsl0-dev and libatlas-base-dev as new build-dependency
+ remove libpdl-stats-perl as (build-)dependency
2012-06-09 - Vincent Danjean <vdanjean@debian.org>
altree (1.2.1-1) unstable; urgency=low
[ Andreas Tille ]
* debian/upstream: Add eprint
* debian/reference: Removed in favour of debian/upstream
[ Vincent Danjean ]
* New (stable) upstream release 1.2.1
* debian/{README.Debian,watch}: No need to skip old last version 1.1.1
* debian/patches/*: latex bug fixed upstream
2012-04-22 - Andreas Tille <tille@debian.org>
altree (1.0.1-7) unstable; urgency=low
[ Thorsten Alteholz ]
* debian/rules: target get-orig-source added
[ Charles Plessy ]
* Renamed debian/upstream-metadata.yaml to debian/upstream
[ Andreas Tille ]
* debian/upstream: Single Reference field instead of Reference-*
* debian/watch: Do not download version 1.1.1 as the author has
asked for in
http://lists.debian.org/debian-med/2009/08/msg00104.html
* debian/README.Debian: Document the "do not package new version"
issue
* debian/control: Standards-Version: 3.9.3 (no changes needed)
* debian/changelog: Verified DEP5 using
cme fix dpkg-copyright
* debian/patches/build-with-recent-tetex.patch: Drop dvips option
Closes: #669551
* debhelper 9 (control+compat)
2011-09-27 - Charles Plessy <plessy@debian.org>
altree (1.0.1-5) unstable; urgency=low
* Upload source package without 3.0 (quilt) autopatch leftover.
Closes: #643045. 
* Corrected VCS URLs in debian/control.
* Use Debhelper 8 (debian/control, debian/compat). 
* Converted debian/copyright to machine-readable format 1.0 (DEP 5).
* Compress binary packages with xz (debian/rules).
* Conforms with Policy 3.9.2 (debian/control, no other changes needed).

See Also

Package Description
altree_1.3.1-2+b1_amd64.deb program to perform phylogeny-based association and localization analysis
alure-doc_1.2-6_all.deb AL Utilities REtooled (documentation)
alure-utils_1.2-6_amd64.deb AL Utilities REtooled (utilities)
am-utils-doc_6.2+rc20110530-3.2_all.deb automounter utilities documentation
am-utils_6.2+rc20110530-3.2_amd64.deb automounter utilities from 4.4BSD (includes amd)
amanda-client_3.3.6-4_amd64.deb Advanced Maryland Automatic Network Disk Archiver (Client)
amanda-common_3.3.6-4_amd64.deb Advanced Maryland Automatic Network Disk Archiver (Libs)
amanda-server_3.3.6-4_amd64.deb Advanced Maryland Automatic Network Disk Archiver (Server)
amap-align_2.2-4_amd64.deb Protein multiple alignment by sequence annealing
amarok-common_2.8.0-2.1_all.deb architecture independent files for Amarok
amarok-doc_2.8.0-2.1_all.deb Amarok documentation (Handbook)
amarok-utils_2.8.0-2.1+b1_amd64.deb utilities for Amarok media player
amarok_2.8.0-2.1+b1_amd64.deb easy to use media player based on the KDE Platform
amavisd-milter_1.5.0-5_amd64.deb amavisd-new interface for milter-capable MTAs
amavisd-new_2.10.1-2~deb8u1_all.deb Interface between MTA and virus scanner/content filters
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