.gitignore
ALTree/Base.pm
ALTree/Chi2.pm
ALTree/Foret.pm
ALTree/Import.pm
ALTree/Input.pm
ALTree/Nanova.pm
ALTree/Node.pm
ALTree/Sens.pm
ALTree/Site.pm
ALTree/SiteCollection.pm
ALTree/SitePerForet.pm
ALTree/SitePerTree.pm
ALTree/SiteSens.pm
ALTree/SiteSensPerForet.pm
ALTree/SiteSensPerTree.pm
ALTree/to_rewrite.pm
ALTree/Tree.pm
ALTree/Utils.pm
bash_completion
Changes
CUtils/c_sources/chisq.c
CUtils/c_sources/chisq.h
CUtils/c_sources/datatype.h
CUtils/c_sources/debug.h
CUtils/c_sources/double_permutation.c
CUtils/c_sources/double_permutation.h
CUtils/c_sources/fisher.c
CUtils/c_sources/fisher.h
CUtils/c_sources/Makefile.PL
CUtils/c_sources/mt19937ar.c
CUtils/c_sources/mt19937ar.h
CUtils/c_sources/MYMETA.json
CUtils/c_sources/myrand.c
CUtils/c_sources/myrand.h
CUtils/c_sources/resampling.c
CUtils/c_sources/resampling.h
CUtils/c_sources/rhyper.c
CUtils/c_sources/rhyper.h
CUtils/c_sources/stats.c
CUtils/c_sources/stats.h
CUtils/c_sources/z.c
CUtils/c_sources/z.h
CUtils/const-c.inc
CUtils/const-xs.inc
CUtils/CUtils.xs
CUtils/fallback/const-c.inc
CUtils/fallback/const-xs.inc
CUtils/lib/ALTree/CUtils.pm
CUtils/Makefile.PL
CUtils/MYMETA.json
CUtils/ppport.h
CUtils/t/ALTree-CUtils.t
CUtils/t/double_permutation.t
Documentation/fig/altree-q.fig
Documentation/fig/anc_outg.fig
Documentation/fig/association_paml.fig
Documentation/fig/association_paup.fig
Documentation/fig/association_phylip.fig
Documentation/fig/create_file_paup.fig
Documentation/fig/create_file_phy.fig
Documentation/fig/localisation_paml.fig
Documentation/fig/localisation_paup.fig
Documentation/fig/option_b.fig
Documentation/fig/option_b.subfig
Documentation/fig/overview.fig
Documentation/Makefile
Documentation/manual.tex
Documentation/stage.bib
Makefile.PL
MANIFEST			This list of files
MYMETA.json
progs/altree
progs/altree-add-S
progs/altree-convert
README
t/ALTree.t
test/create_file/paup_file/caco.phase
test/create_file/paup_file/caco.phase.out
test/create_file/paup_file/caco.phase.out_freqs
test/create_file/paup_file/caco.phase.out_monitor
test/create_file/paup_file/caco.phase.out_pairs
test/create_file/paup_file/caco.phase.out_recom
test/create_file/paup_file/caco.prepaup
test/create_file/paup_file/create_file
test/create_file/paup_file/nb_cas_control.txt
test/create_file/phy-paml_file/create_file
test/create_file/phy-paml_file/fam19_0
test/create_file/phy-paml_file/fam19_0.gm
test/create_file/phy-paml_file/fam19_0_H1_HAPLOTYPES
test/create_file/phy-paml_file/fam19_0_LDmeasuresCASES.xt
test/create_file/phy-paml_file/fam19_0_LDmeasuresCONTROLS.xt
test/create_file/phy-paml_file/nb_cas_control.txt
test/create_file/phy-paml_file/NUM
test/create_file/phy-paml_file/trio.fmh
test/create_file/phy-paml_file/trio.phy
test/create_file/phy-paml_file/trio.prephy
test/paml/tree_building_using_phyML/run_phyML
test/paml/tree_building_using_phyML/trio2.phy
test/paml/tree_building_using_phyML/trio2.phy_phyml_lk.txt
test/paml/tree_building_using_phyML/trio2.phy_phyml_stat.txt
test/paml/tree_building_using_phyML/trio2.phy_phyml_tree.txt
test/paml/unrooted_absent/association/1_trio_ML.asso
test/paml/unrooted_absent/association/2base.t
test/paml/unrooted_absent/association/baseml.ctl
test/paml/unrooted_absent/association/lnf
test/paml/unrooted_absent/association/mlb
test/paml/unrooted_absent/association/nb_cas_control.txt
test/paml/unrooted_absent/association/rst
test/paml/unrooted_absent/association/rst1
test/paml/unrooted_absent/association/rub
test/paml/unrooted_absent/association/run_altree
test/paml/unrooted_absent/association/trio2.phy
test/paml/unrooted_absent/association/trio2.phy_phyml_tree.txt
test/paml/unrooted_present/association/1_trio_ML.asso
test/paml/unrooted_present/association/2base.t
test/paml/unrooted_present/association/baseml.ctl
test/paml/unrooted_present/association/lnf
test/paml/unrooted_present/association/mlb
test/paml/unrooted_present/association/nb_cas_control.txt
test/paml/unrooted_present/association/rst
test/paml/unrooted_present/association/rst1
test/paml/unrooted_present/association/rub
test/paml/unrooted_present/association/run_altree
test/paml/unrooted_present/association/trio2.phy
test/paml/unrooted_present/association/trio2.phy_phyml_tree.txt
test/paml/unrooted_present/localisation/2base.t
test/paml/unrooted_present/localisation/baseml.ctl
test/paml/unrooted_present/localisation/et_trio2.phy
test/paml/unrooted_present/localisation/lnf
test/paml/unrooted_present/localisation/mlb
test/paml/unrooted_present/localisation/nb_cas_controls.txt
test/paml/unrooted_present/localisation/rst
test/paml/unrooted_present/localisation/rst1
test/paml/unrooted_present/localisation/rub
test/paml/unrooted_present/localisation/run-prog
test/paml/unrooted_present/localisation/trio2.loc
test/paml/unrooted_present/localisation/trio2.phy
test/paml/unrooted_present/localisation/trio2.phy_phyml_tree.txt
test/paup/ancestor_absent/association/1_caco.asso
test/paup/ancestor_absent/association/caco.paup
test/paup/ancestor_absent/association/nb_cas_control.txt
test/paup/ancestor_absent/association/run_altree
test/paup/ancestor_absent/association/test.res.log
test/paup/ancestor_absent/association/test.tree
test/paup/ancestor_absent/localisation/caco.loc
test/paup/ancestor_absent/localisation/caco.paup
test/paup/ancestor_absent/localisation/et_caco.paup
test/paup/ancestor_absent/localisation/nb_cas_control.txt
test/paup/ancestor_absent/localisation/run-prog
test/paup/ancestor_absent/localisation/test.res.log
test/paup/ancestor_absent/localisation/test.tree
test/paup/ancestor_present/association/1_caco.asso
test/paup/ancestor_present/association/caco.paup
test/paup/ancestor_present/association/nb_cas_control.txt
test/paup/ancestor_present/association/run_altree
test/paup/ancestor_present/association/test.res.log
test/paup/ancestor_present/association/test.tree
test/paup/ancestor_present/localisation/caco.loc
test/paup/ancestor_present/localisation/caco.paup
test/paup/ancestor_present/localisation/et_caco.paup
test/paup/ancestor_present/localisation/nb_cas_control.txt
test/paup/ancestor_present/localisation/run-prog
test/paup/ancestor_present/localisation/test.res.log
test/paup/ancestor_present/localisation/test.tree
test/paup/outgr_absent/association/1_caco.asso
test/paup/outgr_absent/association/caco.paup
test/paup/outgr_absent/association/nb_cas_control.txt
test/paup/outgr_absent/association/run_altree
test/paup/outgr_absent/association/test.res.log
test/paup/outgr_absent/association/test.tree
test/paup/outgr_absent/localisation/caco.loc
test/paup/outgr_absent/localisation/caco.paup
test/paup/outgr_absent/localisation/et_caco.paup
test/paup/outgr_absent/localisation/nb_cas_control.txt
test/paup/outgr_absent/localisation/run-prog
test/paup/outgr_absent/localisation/test.res.log
test/paup/outgr_absent/localisation/test.tree
test/paup/outgr_present/association/1_caco.asso
test/paup/outgr_present/association/caco.paup
test/paup/outgr_present/association/nb_cas_control.txt
test/paup/outgr_present/association/run_altree
test/paup/outgr_present/association/test.res.log
test/paup/outgr_present/association/test.tree
test/paup/outgr_present/localisation/caco.loc
test/paup/outgr_present/localisation/caco.paup
test/paup/outgr_present/localisation/et_caco.paup
test/paup/outgr_present/localisation/nb_cas_control.txt
test/paup/outgr_present/localisation/run-prog
test/paup/outgr_present/localisation/test.res.log
test/paup/outgr_present/localisation/test.tree
test/paup/unrooted_absent/association/1_caco.asso
test/paup/unrooted_absent/association/caco.paup
test/paup/unrooted_absent/association/nb_cas_control.txt
test/paup/unrooted_absent/association/run_altree
test/paup/unrooted_absent/association/test.res.log
test/paup/unrooted_absent/association/test.tree
test/paup/unrooted_absent/localisation/caco.loc
test/paup/unrooted_absent/localisation/caco.paup
test/paup/unrooted_absent/localisation/et_caco.paup
test/paup/unrooted_absent/localisation/nb_cas_control.txt
test/paup/unrooted_absent/localisation/run-prog
test/paup/unrooted_absent/localisation/test.res.log
test/paup/unrooted_absent/localisation/test.tree
test/paup/unrooted_present/association/1_caco.asso
test/paup/unrooted_present/association/caco.paup
test/paup/unrooted_present/association/nb_cas_control.txt
test/paup/unrooted_present/association/run_altree
test/paup/unrooted_present/association/test.res.log
test/paup/unrooted_present/association/test.tree
test/paup/unrooted_present/localisation/caco.loc
test/paup/unrooted_present/localisation/caco.paup
test/paup/unrooted_present/localisation/et_caco.paup
test/paup/unrooted_present/localisation/nb_cas_control.txt
test/paup/unrooted_present/localisation/run-prog
test/paup/unrooted_present/localisation/test.res.log
test/paup/unrooted_present/localisation/test.tree
test/phylip/ancestor_absent/association/1_trio_phy.asso
test/phylip/ancestor_absent/association/ancestors
test/phylip/ancestor_absent/association/nb_cas_controls.txt
test/phylip/ancestor_absent/association/outfile
test/phylip/ancestor_absent/association/outtree
test/phylip/ancestor_absent/association/run_altree
test/phylip/ancestor_absent/association/trio.phy
test/phylip/ancestor_present/association/1_trio_phy.asso
test/phylip/ancestor_present/association/ancestors
test/phylip/ancestor_present/association/nb_cas_controls.txt
test/phylip/ancestor_present/association/outfile
test/phylip/ancestor_present/association/outtree
test/phylip/ancestor_present/association/run_altree
test/phylip/ancestor_present/association/trio.phy
test/phylip/outgroup_absent/association/1_trio_phy.asso
test/phylip/outgroup_absent/association/nb_cas_controls.txt
test/phylip/outgroup_absent/association/outfile
test/phylip/outgroup_absent/association/outtree
test/phylip/outgroup_absent/association/run_altree
test/phylip/outgroup_absent/association/trio.phy
test/phylip/outgroup_present/association/1_trio_phy.asso
test/phylip/outgroup_present/association/nb_cas_controls.txt
test/phylip/outgroup_present/association/outfile
test/phylip/outgroup_present/association/outtree
test/phylip/outgroup_present/association/run_altree
test/phylip/outgroup_present/association/trio.phy
