diff --git a/Documentation/manual.tex b/Documentation/manual.tex
index a6446d006153be599efdd3747cc6a11444771f30..59a519e7a603ca375a9f439e1bc4b7255a9c0321 100644
--- a/Documentation/manual.tex
+++ b/Documentation/manual.tex
@@ -91,7 +91,7 @@
phylogenetic Trees }
\author{Claire Bardel, Vincent Danjean, Pierre Darlu and Emmanuelle Génin}
-\date{Version 1.1.0}
+\date{Version 1.2}
\maketitle
\tableofcontents
@@ -101,6 +101,8 @@
\chapter{Introduction}
\section{What's new?}
+\paragraph{Problem with PAUP*}
+It seems that PAUP* does not run anymore on recent versions of Linux. We have not tested windows or MacOS version. If PAUP* does not work on your system, example files using PAUP* (in the paup directory) will not run because PAUP* output files will not be produced.
\paragraph{Version 1.1.0: modification of \newchitree and \etHT to deal with quantitative data}
The software now deals with quantitative data. For the association test, series of one-way ANOVA are performed instead of the homogeneity tests. For the localisation test, only the definition of the S character is different for quantitative traits. Currently, \rechaplo has not been modified and does not deal with quantitative data.
diff --git a/Makefile.PL b/Makefile.PL
index 694f309286b9c73a961641a5ed94f46feef2e2b2..75fbb52b8f661323005989e49cef2c1513e7a38b 100644
--- a/Makefile.PL
+++ b/Makefile.PL
@@ -6,7 +6,7 @@ WriteMakefile(
NAME => 'altree',
PMLIBDIRS => [ 'ALTree' ],
DIR => [ 'CUtils' ],
- VERSION => '1.1.1',
+ VERSION => '1.2',
LICENSE => 'perl',
PREREQ_PM => {}, # e.g., Module::Name => 1.1
($] >= 5.005 ? ## Add these new keywords supported since 5.005
diff --git a/test/phylip/ancestor_absent/association/1_trio_phy.asso b/test/phylip/ancestor_absent/association/1_trio_phy.asso
index 6879c601c31f9ba9470d4428a7c2873d2e263c9c..631b226dcd509ec5edc66484bee889138e839e8f 100644
--- a/test/phylip/ancestor_absent/association/1_trio_phy.asso
+++ b/test/phylip/ancestor_absent/association/1_trio_phy.asso
@@ -1,9 +1,9 @@
- /----* H030 case/control:1/1
+ /----* H030 (LEVEL: 1) case/control:1/1
| Site: 9 Sens: 0-->1
- |----* H006 case/control:23/19
+ |----* H006 (LEVEL: 1) case/control:23/19
| Site: 2 Sens: 1-->0
------* 10+(27)+(1) case/control:200/200
+-----* 10+(27)+(1) (LEVEL: 0) case/control:200/200
|
| [0] ddl=3 chi2=0.52 p_value_chi2=0.86
| [1] ddl=6 chi2=4.29 p_value_chi2=0.674
@@ -19,94 +19,94 @@
| [11] ddl=28 chi2=59.22 p_value_chi2=0
| [12] ddl=31 chi2=61.68 p_value_chi2=0
| [13] ddl=34 chi2=68.34 p_value_chi2=0
- | /----* H035 case/control:1/0
+ | /----* H035 (LEVEL: 2) case/control:1/0
| | Site: 10 Sens: 1-->0
- | |----* H007 case/control:25/36
- |----* 17+(22) case/control:54/58
+ | |----* H007 (LEVEL: 2) case/control:25/36
+ |----* 17+(22) (LEVEL: 1) case/control:54/58
| | Site: 4 Sens: 0-->1
- | | /----* H023 case/control:1/5
- | | | /----* H021 case/control:11/2
+ | | /----* H023 (LEVEL: 3) case/control:1/5
+ | | | /----* H021 (LEVEL: 5) case/control:11/2
| | | | Site: 1 Sens: 1-->0
| | | | Site: 5 Sens: 0-->1
- | | | /----* 26 case/control:16/12
+ | | | /----* 26 (LEVEL: 4) case/control:16/12
| | | | | Site: 8 Sens: 0-->1
- | | | | \----* H009 case/control:5/10
- | | | |----* H012 case/control:1/2
- | | |----* 16+(29) case/control:26/17
+ | | | | \----* H009 (LEVEL: 5) case/control:5/10
+ | | | |----* H012 (LEVEL: 4) case/control:1/2
+ | | |----* 16+(29) (LEVEL: 3) case/control:26/17
| | | | Site: 6 Sens: 1-->0
- | | | \----* H002 case/control:9/3
+ | | | \----* H002 (LEVEL: 4) case/control:9/3
| | | Site: 5 Sens: 0-->1
- | \----* 6+(8) case/control:28/22
+ | \----* 6+(8) (LEVEL: 2) case/control:28/22
| | Site: 3 Sens: 0-->1
- | \----* H026 case/control:1/0
+ | \----* H026 (LEVEL: 3) case/control:1/0
| Site: 1 Sens: 1-->0
- | /----* H025 case/control:2/3
- \----* 25 case/control:122/122
+ | /----* H025 (LEVEL: 2) case/control:2/3
+ \----* 25 (LEVEL: 1) case/control:122/122
| Site: 1 Sens: 1-->0
- | /----* H004 case/control:11/2
- \----* 2 case/control:120/119
+ | /----* H004 (LEVEL: 3) case/control:11/2
+ \----* 2 (LEVEL: 2) case/control:120/119
| Site: 5 Sens: 0-->1
- | /----* H005 case/control:2/2
+ | /----* H005 (LEVEL: 4) case/control:2/2
| | Site: 10 Sens: 1-->0
- | |----* H008 case/control:28/19
- | |----* H031 case/control:1/0
+ | |----* H008 (LEVEL: 4) case/control:28/19
+ | |----* H031 (LEVEL: 4) case/control:1/0
| | Site: 8 Sens: 0-->1
- \----* 19+(30)+(7+(28)) case/control:109/117
+ \----* 19+(30)+(7+(28)) (LEVEL: 3) case/control:109/117
| Site: 6 Sens: 1-->0
- | /----* H032 case/control:0/1
+ | /----* H032 (LEVEL: 5) case/control:0/1
| | Site: 7 Sens: 0-->1
- |----* 24 case/control:2/3
+ |----* 24 (LEVEL: 4) case/control:2/3
| | Site: 4 Sens: 0-->1
- | \----* H016 case/control:2/2
- | /----* H024 case/control:1/0
- \----* 14 case/control:76/93
+ | \----* H016 (LEVEL: 5) case/control:2/2
+ | /----* H024 (LEVEL: 5) case/control:1/0
+ \----* 14 (LEVEL: 4) case/control:76/93
| Site: 9 Sens: 0-->1
- | /----* H013 case/control:15/5
- | /----* 23 case/control:72/90
+ | /----* H013 (LEVEL: 7) case/control:15/5
+ | /----* 23 (LEVEL: 6) case/control:72/90
| | | Site: 10 Sens: 1-->0
- | | | /----* H022 case/control:9/1
- | | \----* 32 case/control:57/85
+ | | | /----* H022 (LEVEL: 8) case/control:9/1
+ | | \----* 32 (LEVEL: 7) case/control:57/85
| | | Site: 6 Sens: 0-->1
- | | | /----* H029 case/control:1/3
+ | | | /----* H029 (LEVEL: 9) case/control:1/3
| | | | Site: 10 Sens: 0-->1
- | | | |----* H034 case/control:1/0
- | | \----* 4+(20) case/control:48/84
+ | | | |----* H034 (LEVEL: 9) case/control:1/0
+ | | \----* 4+(20) (LEVEL: 8) case/control:48/84
| | | Site: 5 Sens: 1-->0
- | | | /----* H033 case/control:0/1
- | | \----* 18 case/control:46/81
+ | | | /----* H033 (LEVEL: 10) case/control:0/1
+ | | \----* 18 (LEVEL: 9) case/control:46/81
| | | Site: 4 Sens: 0-->1
- | | | /----* H010 case/control:1/3
- | | \----* 12 case/control:46/80
+ | | | /----* H010 (LEVEL: 11) case/control:1/3
+ | | \----* 12 (LEVEL: 10) case/control:46/80
| | | Site: 1 Sens: 0-->1
- | | | /----* H011 case/control:3/8
- | | | |----* H003 case/control:2/0
+ | | | /----* H011 (LEVEL: 12) case/control:3/8
+ | | | |----* H003 (LEVEL: 12) case/control:2/0
| | | | Site: 5 Sens: 0-->1
- | | \----* 21+(31)+(5) case/control:45/77
+ | | \----* 21+(31)+(5) (LEVEL: 11) case/control:45/77
| | | Site: 10 Sens: 0-->1
- | | | /----* H014 case/control:2/3
+ | | | /----* H014 (LEVEL: 13) case/control:2/3
| | | | Site: 1 Sens: 1-->0
- | | | |----* H017 case/control:0/8
- | | |----* 33+(15) case/control:3/13
+ | | | |----* H017 (LEVEL: 13) case/control:0/8
+ | | |----* 33+(15) (LEVEL: 12) case/control:3/13
| | | | Site: 3 Sens: 0-->1
- | | | \----* H027 case/control:1/2
+ | | | \----* H027 (LEVEL: 13) case/control:1/2
| | | Site: 6 Sens: 1-->0
| | | Site: 10 Sens: 1-->0
- | | | /----* H018 case/control:2/2
- | | \----* 34 case/control:37/56
+ | | | /----* H018 (LEVEL: 13) case/control:2/2
+ | | \----* 34 (LEVEL: 12) case/control:37/56
| | | Site: 4 Sens: 1-->0
- | | | /----* H028 case/control:4/0
+ | | | /----* H028 (LEVEL: 14) case/control:4/0
| | | | Site: 8 Sens: 1-->0
- | | | |----* H001 case/control:24/39
- | | \----* 11+(13)+(9) case/control:35/54
+ | | | |----* H001 (LEVEL: 14) case/control:24/39
+ | | \----* 11+(13)+(9) (LEVEL: 13) case/control:35/54
| | | Site: 2 Sens: 1-->0
- | | |----* H015 case/control:2/6
+ | | |----* H015 (LEVEL: 14) case/control:2/6
| | | Site: 9 Sens: 1-->0
- | | \----* H020 case/control:5/9
+ | | \----* H020 (LEVEL: 14) case/control:5/9
| | Site: 10 Sens: 1-->0
- \----* 3 case/control:75/93
+ \----* 3 (LEVEL: 5) case/control:75/93
| Site: 8 Sens: 0-->1
| Site: 7 Sens: 0-->1
- \----* H019 case/control:3/3
+ \----* H019 (LEVEL: 6) case/control:3/3
Number of permutation: 1
diff --git a/test/phylip/ancestor_absent/association/outfile b/test/phylip/ancestor_absent/association/outfile
index d1a74c19976a5e233005762d76c61e67cfc97dde..f652795a526a1c59ff37a4d2e99c2790b60a9469 100644
--- a/test/phylip/ancestor_absent/association/outfile
+++ b/test/phylip/ancestor_absent/association/outfile
@@ -1,5 +1,5 @@
-Mixed parsimony algorithm, version 3.63
+Mixed parsimony algorithm, version 3.69
Wagner parsimony method
diff --git a/test/phylip/ancestor_absent/association/run_altree b/test/phylip/ancestor_absent/association/run_altree
index 1397fa317556db984fcd747444524c0abaa94077..7d8360231b8b738b9312e6205c28c8c2b12ebb66 100755
--- a/test/phylip/ancestor_absent/association/run_altree
+++ b/test/phylip/ancestor_absent/association/run_altree
@@ -8,6 +8,6 @@ phylip mix
# have to specify it with the --anc-seq option
# Only one permutation is performed...
-../../../../altree -i outfile -j nb_cas_controls.txt \
- -a -t SNP -p phylip -r 1 \
- --tree-to-analyse 1 --anc-seq 1100010001 -o 1_trio_phy.asso
+altree -i outfile -j nb_cas_controls.txt \
+-a -t SNP -p phylip -r 1 --data-qual qualitative \
+--tree-to-analyse 1 --anc-seq 1100010001 -o 1_trio_phy.asso
diff --git a/test/phylip/ancestor_present/association/1_trio_phy.asso b/test/phylip/ancestor_present/association/1_trio_phy.asso
index 8f421679c3df6e84012521dda3892e713799add6..50d0e8b3e2556730942791e0c19a87e263a57860 100644
--- a/test/phylip/ancestor_present/association/1_trio_phy.asso
+++ b/test/phylip/ancestor_present/association/1_trio_phy.asso
@@ -1,48 +1,48 @@
- /----* H035 case/control:1/0
+ /----* H035 (LEVEL: 2) case/control:1/0
| Site: 10 Sens: 1-->0
- /----* 22 case/control:26/36
+ /----* 22 (LEVEL: 1) case/control:26/36
| | Site: 4 Sens: 0-->1
- | \----* H007 case/control:25/36
- | /----* H025 case/control:2/3
- |----* 25 case/control:75/51
+ | \----* H007 (LEVEL: 2) case/control:25/36
+ | /----* H025 (LEVEL: 2) case/control:2/3
+ |----* 25 (LEVEL: 1) case/control:75/51
| | Site: 1 Sens: 1-->0
- | | /----* H004 case/control:11/2
- | \----* 2 case/control:73/48
+ | | /----* H004 (LEVEL: 3) case/control:11/2
+ | \----* 2 (LEVEL: 2) case/control:73/48
| | Site: 5 Sens: 0-->1
- | | /----* H005 case/control:2/2
+ | | /----* H005 (LEVEL: 4) case/control:2/2
| | | Site: 10 Sens: 1-->0
- | | |----* H031 case/control:1/0
+ | | |----* H031 (LEVEL: 4) case/control:1/0
| | | Site: 8 Sens: 0-->1
- | | |----* H008 case/control:28/19
- | \----* 19+(30+(28))+(14) case/control:62/46
+ | | |----* H008 (LEVEL: 4) case/control:28/19
+ | \----* 19+(30+(28))+(14) (LEVEL: 3) case/control:62/46
| | Site: 6 Sens: 1-->0
- | |----* H024 case/control:1/0
+ | |----* H024 (LEVEL: 4) case/control:1/0
| | Site: 9 Sens: 0-->1
- | | /----* H032 case/control:0/1
+ | | /----* H032 (LEVEL: 5) case/control:0/1
| | | Site: 7 Sens: 0-->1
- | | |----* H016 case/control:2/2
- | \----* 7+(24) case/control:30/25
+ | | |----* H016 (LEVEL: 5) case/control:2/2
+ | \----* 7+(24) (LEVEL: 4) case/control:30/25
| | Site: 4 Sens: 0-->1
- | | /----* H021 case/control:11/2
+ | | /----* H021 (LEVEL: 6) case/control:11/2
| | | Site: 8 Sens: 0-->1
- | \----* 26 case/control:28/22
+ | \----* 26 (LEVEL: 5) case/control:28/22
| | Site: 3 Sens: 0-->1
- | | /----* H002 case/control:9/3
- | \----* 8 case/control:17/20
+ | | /----* H002 (LEVEL: 7) case/control:9/3
+ | \----* 8 (LEVEL: 6) case/control:17/20
| | Site: 1 Sens: 0-->1
- | | /----* H012 case/control:1/2
- | | |----* H009 case/control:5/10
+ | | /----* H012 (LEVEL: 8) case/control:1/2
+ | | |----* H009 (LEVEL: 8) case/control:5/10
| | | Site: 8 Sens: 0-->1
- | \----* 16+(29) case/control:8/17
+ | \----* 16+(29) (LEVEL: 7) case/control:8/17
| | Site: 5 Sens: 1-->0
- | | /----* H023 case/control:1/5
- | \----* 6 case/control:2/5
+ | | /----* H023 (LEVEL: 9) case/control:1/5
+ | \----* 6 (LEVEL: 8) case/control:2/5
| | Site: 6 Sens: 0-->1
- | \----* H026 case/control:1/0
+ | \----* H026 (LEVEL: 9) case/control:1/0
| Site: 1 Sens: 1-->0
- |----* ANCE case/control:4/4
------* 1+(17)+(27+(35)) case/control:204/204
+ |----* ANCE (LEVEL: 1) case/control:4/4
+-----* 1+(17)+(27+(35)) (LEVEL: 0) case/control:204/204
|
| [0] ddl=4 chi2=7.12 p_value_chi2=0.105
| [1] ddl=7 chi2=10.66 p_value_chi2=0.131
@@ -53,56 +53,56 @@
| [6] ddl=30 chi2=63.51 p_value_chi2=0
| [7] ddl=33 chi2=64.80 p_value_chi2=0
| [8] ddl=35 chi2=68.34 p_value_chi2=0
- |----* H030 case/control:1/1
+ |----* H030 (LEVEL: 1) case/control:1/1
| Site: 9 Sens: 0-->1
- | /----* H006 case/control:23/19
- \----* 10 case/control:98/112
+ | /----* H006 (LEVEL: 2) case/control:23/19
+ \----* 10 (LEVEL: 1) case/control:98/112
| Site: 2 Sens: 1-->0
- | /----* H028 case/control:4/0
- \----* 13 case/control:75/93
+ | /----* H028 (LEVEL: 3) case/control:4/0
+ \----* 13 (LEVEL: 2) case/control:75/93
| Site: 7 Sens: 0-->1
| Site: 9 Sens: 0-->1
- | /----* H015 case/control:2/6
+ | /----* H015 (LEVEL: 4) case/control:2/6
| | Site: 9 Sens: 1-->0
- | |----* H001 case/control:24/39
- \----* 3+(9+(11)) case/control:71/93
+ | |----* H001 (LEVEL: 4) case/control:24/39
+ \----* 3+(9+(11)) (LEVEL: 3) case/control:71/93
| Site: 8 Sens: 0-->1
- |----* H020 case/control:5/9
+ |----* H020 (LEVEL: 4) case/control:5/9
| Site: 10 Sens: 1-->0
- | /----* H018 case/control:2/2
- | | /----* H011 case/control:3/8
- | | |----* H003 case/control:2/0
+ | /----* H018 (LEVEL: 5) case/control:2/2
+ | | /----* H011 (LEVEL: 6) case/control:3/8
+ | | |----* H003 (LEVEL: 6) case/control:2/0
| | | Site: 5 Sens: 0-->1
- | |----* 21+(31)+(15) case/control:9/25
+ | |----* 21+(31)+(15) (LEVEL: 5) case/control:9/25
| | | Site: 4 Sens: 0-->1
- | | | /----* H014 case/control:2/3
+ | | | /----* H014 (LEVEL: 7) case/control:2/3
| | | | Site: 1 Sens: 1-->0
- | | |----* 33 case/control:2/11
+ | | |----* 33 (LEVEL: 6) case/control:2/11
| | | | Site: 3 Sens: 0-->1
- | | | \----* H017 case/control:0/8
- | | | /----* H010 case/control:1/3
- | | | |----* H033 case/control:0/1
+ | | | \----* H017 (LEVEL: 7) case/control:0/8
+ | | | /----* H010 (LEVEL: 7) case/control:1/3
+ | | | |----* H033 (LEVEL: 7) case/control:0/1
| | | | Site: 1 Sens: 1-->0
- | | \----* 12+(18) case/control:2/6
+ | | \----* 12+(18) (LEVEL: 6) case/control:2/6
| | | Site: 10 Sens: 1-->0
- | | \----* H027 case/control:1/2
+ | | \----* H027 (LEVEL: 7) case/control:1/2
| | Site: 6 Sens: 1-->0
| | Site: 3 Sens: 0-->1
- \----* 5+(34) case/control:40/39
+ \----* 5+(34) (LEVEL: 4) case/control:40/39
| Site: 2 Sens: 0-->1
- | /----* H029 case/control:1/3
- \----* 20 case/control:29/12
+ | /----* H029 (LEVEL: 6) case/control:1/3
+ \----* 20 (LEVEL: 5) case/control:29/12
| Site: 1 Sens: 1-->0
- | /----* H034 case/control:1/0
- \----* 4 case/control:28/9
+ | /----* H034 (LEVEL: 7) case/control:1/0
+ \----* 4 (LEVEL: 6) case/control:28/9
| Site: 10 Sens: 1-->0
- | /----* H022 case/control:9/1
- \----* 32 case/control:27/9
+ | /----* H022 (LEVEL: 8) case/control:9/1
+ \----* 32 (LEVEL: 7) case/control:27/9
| Site: 5 Sens: 0-->1
- | /----* H013 case/control:15/5
- \----* 23 case/control:18/8
+ | /----* H013 (LEVEL: 9) case/control:15/5
+ \----* 23 (LEVEL: 8) case/control:18/8
| Site: 6 Sens: 1-->0
- \----* H019 case/control:3/3
+ \----* H019 (LEVEL: 9) case/control:3/3
Site: 10 Sens: 0-->1
Number of permutation: 1
diff --git a/test/phylip/ancestor_present/association/outfile b/test/phylip/ancestor_present/association/outfile
index e8a122b44ab3bf32e1e553b107d29a0fc422ac0f..3f89f1ffb10a9646a8010c9d8aebc0668d0957fe 100644
--- a/test/phylip/ancestor_present/association/outfile
+++ b/test/phylip/ancestor_present/association/outfile
@@ -1,5 +1,5 @@
-Mixed parsimony algorithm, version 3.63
+Mixed parsimony algorithm, version 3.69
Wagner parsimony method
diff --git a/test/phylip/ancestor_present/association/run_altree b/test/phylip/ancestor_present/association/run_altree
index 51a135cac157bfd7dd4adca61ff8749ea3c89962..fe366561e9b99c97af12f26198e50b437e5b792e 100755
--- a/test/phylip/ancestor_present/association/run_altree
+++ b/test/phylip/ancestor_present/association/run_altree
@@ -6,6 +6,6 @@ phylip mix
# To perform the association test. The ancestral sequence must be
# provided with the --anc-seq option beacuse it is not in the phylip
# output file
-../../../../altree -i outfile -j nb_cas_controls.txt \
- -a -t SNP -p phylip -r 1 \
+ altree -i outfile -j nb_cas_controls.txt \
+ -a -t SNP -p phylip -r 1 --data-qual qualitative\
--tree-to-analyse 1 --anc-seq 1100010001 -o 1_trio_phy.asso
diff --git a/test/phylip/outgroup_absent/association/1_trio_phy.asso b/test/phylip/outgroup_absent/association/1_trio_phy.asso
index fda8270ce0f406d92b6b637c18c43b9a68332c37..6f7e09bd8a05a762441432f59ba368432b3d55bf 100644
--- a/test/phylip/outgroup_absent/association/1_trio_phy.asso
+++ b/test/phylip/outgroup_absent/association/1_trio_phy.asso
@@ -1,9 +1,9 @@
- /----* H030 case/control:1/1
+ /----* H030 (LEVEL: 1) case/control:1/1
| Site: 9 Sens: 0-->1
- |----* H006 case/control:23/19
+ |----* H006 (LEVEL: 1) case/control:23/19
| Site: 2 Sens: 1-->0
------* 35+(10+(27)) case/control:200/200
+-----* 35+(10+(27)) (LEVEL: 0) case/control:200/200
|
| [0] ddl=2 chi2=0.43 p_value_chi2=0.801
| [1] ddl=4 chi2=3.49 p_value_chi2=0.539
@@ -22,94 +22,94 @@
| [14] ddl=27 chi2=54.70 p_value_chi2=0
| [15] ddl=32 chi2=66.05 p_value_chi2=0
| [16] ddl=34 chi2=68.34 p_value_chi2=0
- | /----* H035 case/control:1/0
+ | /----* H035 (LEVEL: 2) case/control:1/0
| | Site: 10 Sens: 1-->0
- | |----* H007 case/control:25/36
- \----* 17+(22) case/control:176/180
+ | |----* H007 (LEVEL: 2) case/control:25/36
+ \----* 17+(22) (LEVEL: 1) case/control:176/180
| Site: 4 Sens: 0-->1
- | /----* H023 case/control:1/5
- | |----* H026 case/control:1/0
+ | /----* H023 (LEVEL: 3) case/control:1/5
+ | |----* H026 (LEVEL: 3) case/control:1/0
| | Site: 1 Sens: 1-->0
- \----* 1+(6) case/control:150/144
+ \----* 1+(6) (LEVEL: 2) case/control:150/144
| Site: 3 Sens: 0-->1
- | /----* H012 case/control:1/2
- | |----* H009 case/control:5/10
+ | /----* H012 (LEVEL: 4) case/control:1/2
+ | |----* H009 (LEVEL: 4) case/control:5/10
| | Site: 8 Sens: 0-->1
- \----* 16+(29) case/control:148/139
+ \----* 16+(29) (LEVEL: 3) case/control:148/139
| Site: 6 Sens: 1-->0
- | /----* H002 case/control:9/3
- \----* 8 case/control:142/127
+ | /----* H002 (LEVEL: 5) case/control:9/3
+ \----* 8 (LEVEL: 4) case/control:142/127
| Site: 5 Sens: 0-->1
- | /----* H021 case/control:11/2
+ | /----* H021 (LEVEL: 6) case/control:11/2
| | Site: 8 Sens: 0-->1
- \----* 26 case/control:133/124
+ \----* 26 (LEVEL: 5) case/control:133/124
| Site: 1 Sens: 1-->0
- | /----* H032 case/control:0/1
+ | /----* H032 (LEVEL: 7) case/control:0/1
| | Site: 7 Sens: 0-->1
- | |----* H016 case/control:2/2
- \----* 7+(24) case/control:122/122
+ | |----* H016 (LEVEL: 7) case/control:2/2
+ \----* 7+(24) (LEVEL: 6) case/control:122/122
| Site: 3 Sens: 1-->0
- | /----* H025 case/control:2/3
+ | /----* H025 (LEVEL: 9) case/control:2/3
| | Site: 5 Sens: 1-->0
- | /----* 25 case/control:13/5
+ | /----* 25 (LEVEL: 8) case/control:13/5
| | | Site: 6 Sens: 0-->1
- | | \----* H004 case/control:11/2
- | |----* H008 case/control:28/19
- | |----* H005 case/control:2/2
+ | | \----* H004 (LEVEL: 9) case/control:11/2
+ | |----* H008 (LEVEL: 8) case/control:28/19
+ | |----* H005 (LEVEL: 8) case/control:2/2
| | Site: 10 Sens: 1-->0
- \----* 2+(19+(28+(30))) case/control:120/119
+ \----* 2+(19+(28+(30))) (LEVEL: 7) case/control:120/119
| Site: 4 Sens: 1-->0
- |----* H031 case/control:1/0
+ |----* H031 (LEVEL: 8) case/control:1/0
| Site: 8 Sens: 0-->1
- | /----* H024 case/control:1/0
- \----* 14 case/control:76/93
+ | /----* H024 (LEVEL: 9) case/control:1/0
+ \----* 14 (LEVEL: 8) case/control:76/93
| Site: 9 Sens: 0-->1
- | /----* H013 case/control:15/5
- | /----* 23 case/control:72/90
+ | /----* H013 (LEVEL: 11) case/control:15/5
+ | /----* 23 (LEVEL: 10) case/control:72/90
| | | Site: 10 Sens: 1-->0
- | | | /----* H022 case/control:9/1
- | | \----* 32 case/control:57/85
+ | | | /----* H022 (LEVEL: 12) case/control:9/1
+ | | \----* 32 (LEVEL: 11) case/control:57/85
| | | Site: 6 Sens: 0-->1
- | | | /----* H033 case/control:0/1
- | | | /----* 18 case/control:1/4
+ | | | /----* H033 (LEVEL: 14) case/control:0/1
+ | | | /----* 18 (LEVEL: 13) case/control:1/4
| | | | | Site: 4 Sens: 0-->1
- | | | | \----* H010 case/control:1/3
+ | | | | \----* H010 (LEVEL: 14) case/control:1/3
| | | | Site: 1 Sens: 0-->1
- | | | |----* H034 case/control:1/0
- | | \----* 4+(12) case/control:48/84
+ | | | |----* H034 (LEVEL: 13) case/control:1/0
+ | | \----* 4+(12) (LEVEL: 12) case/control:48/84
| | | Site: 5 Sens: 1-->0
- | | | /----* H029 case/control:1/3
- | | \----* 20 case/control:46/80
+ | | | /----* H029 (LEVEL: 14) case/control:1/3
+ | | \----* 20 (LEVEL: 13) case/control:46/80
| | | Site: 10 Sens: 0-->1
- | | | /----* H018 case/control:2/2
- | | | | /----* H011 case/control:3/8
- | | | | |----* H003 case/control:2/0
+ | | | /----* H018 (LEVEL: 15) case/control:2/2
+ | | | | /----* H011 (LEVEL: 16) case/control:3/8
+ | | | | |----* H003 (LEVEL: 16) case/control:2/0
| | | | | Site: 5 Sens: 0-->1
- | | | |----* 21+(31) case/control:8/21
+ | | | |----* 21+(31) (LEVEL: 15) case/control:8/21
| | | | | Site: 4 Sens: 0-->1
- | | | | | /----* H014 case/control:2/3
+ | | | | | /----* H014 (LEVEL: 17) case/control:2/3
| | | | | | Site: 1 Sens: 1-->0
- | | | | | |----* H017 case/control:0/8
- | | | | \----* 15+(33) case/control:3/13
+ | | | | | |----* H017 (LEVEL: 17) case/control:0/8
+ | | | | \----* 15+(33) (LEVEL: 16) case/control:3/13
| | | | | Site: 3 Sens: 0-->1
- | | | | \----* H027 case/control:1/2
+ | | | | \----* H027 (LEVEL: 17) case/control:1/2
| | | | Site: 6 Sens: 1-->0
| | | | Site: 10 Sens: 1-->0
- | | \----* 5+(34) case/control:45/77
+ | | \----* 5+(34) (LEVEL: 14) case/control:45/77
| | | Site: 1 Sens: 0-->1
- | | | /----* H001 case/control:24/39
- | | | |----* H015 case/control:2/6
+ | | | /----* H001 (LEVEL: 16) case/control:24/39
+ | | | |----* H015 (LEVEL: 16) case/control:2/6
| | | | Site: 9 Sens: 1-->0
- | | \----* 9+(11)+(13) case/control:35/54
+ | | \----* 9+(11)+(13) (LEVEL: 15) case/control:35/54
| | | Site: 2 Sens: 1-->0
- | | |----* H028 case/control:4/0
+ | | |----* H028 (LEVEL: 16) case/control:4/0
| | | Site: 8 Sens: 1-->0
- | | \----* H020 case/control:5/9
+ | | \----* H020 (LEVEL: 16) case/control:5/9
| | Site: 10 Sens: 1-->0
- \----* 3 case/control:75/93
+ \----* 3 (LEVEL: 9) case/control:75/93
| Site: 8 Sens: 0-->1
| Site: 7 Sens: 0-->1
- \----* H019 case/control:3/3
+ \----* H019 (LEVEL: 10) case/control:3/3
Number of permutation: 1
diff --git a/test/phylip/outgroup_absent/association/outfile b/test/phylip/outgroup_absent/association/outfile
index e2632ca3168ebf692f7d85641279682c39781638..12fb7de27d7a5bdb10371c422d79ac752a3708ca 100644
--- a/test/phylip/outgroup_absent/association/outfile
+++ b/test/phylip/outgroup_absent/association/outfile
@@ -1,5 +1,5 @@
-Mixed parsimony algorithm, version 3.63
+Mixed parsimony algorithm, version 3.69
Wagner parsimony method
diff --git a/test/phylip/outgroup_absent/association/run_altree b/test/phylip/outgroup_absent/association/run_altree
index 4c6f40bd350a9df0ec787eb6ea636f9dd6de16ce..d09d773734f48eba42d8a889e6a9a2b3a2dab094 100755
--- a/test/phylip/outgroup_absent/association/run_altree
+++ b/test/phylip/outgroup_absent/association/run_altree
@@ -9,6 +9,6 @@ phylip mix
# --remove-outgroup). The name of the outgroup must be specified so that
# the program can identify the outgroup sequence
-../../../../altree -i outfile -j nb_cas_controls.txt \
+altree -i outfile -j nb_cas_controls.txt --data-qual qualitative \
-a -t SNP -p phylip --outgroup OUTG --remove-outgroup -r 1 \
--tree-to-analyse 1 -o 1_trio_phy.asso
diff --git a/test/phylip/outgroup_present/association/1_trio_phy.asso b/test/phylip/outgroup_present/association/1_trio_phy.asso
index a390429fd26489827eea7e1fecdc03c20725a12b..ee4b6daafec102e67ebf46029f5e5aa8127b1f0c 100644
--- a/test/phylip/outgroup_present/association/1_trio_phy.asso
+++ b/test/phylip/outgroup_present/association/1_trio_phy.asso
@@ -1,8 +1,8 @@
- /----* OUTG case/control:4/4
- |----* H030 case/control:1/1
+ /----* OUTG (LEVEL: 1) case/control:4/4
+ |----* H030 (LEVEL: 1) case/control:1/1
| Site: 9 Sens: 0-->1
------* 35+(10+(27)) case/control:204/204
+-----* 35+(10+(27)) (LEVEL: 0) case/control:204/204
|
| [0] ddl=3 chi2=0.43 p_value_chi2=0.948
| [1] ddl=5 chi2=3.49 p_value_chi2=0.696
@@ -21,96 +21,96 @@
| [14] ddl=28 chi2=54.70 p_value_chi2=0.001
| [15] ddl=33 chi2=66.05 p_value_chi2=0
| [16] ddl=35 chi2=68.34 p_value_chi2=0
- |----* H006 case/control:23/19
+ |----* H006 (LEVEL: 1) case/control:23/19
| Site: 2 Sens: 1-->0
- | /----* H035 case/control:1/0
+ | /----* H035 (LEVEL: 2) case/control:1/0
| | Site: 10 Sens: 1-->0
- | |----* H007 case/control:25/36
- \----* 17+(22) case/control:176/180
+ | |----* H007 (LEVEL: 2) case/control:25/36
+ \----* 17+(22) (LEVEL: 1) case/control:176/180
| Site: 4 Sens: 0-->1
- | /----* H023 case/control:1/5
- | |----* H026 case/control:1/0
+ | /----* H023 (LEVEL: 3) case/control:1/5
+ | |----* H026 (LEVEL: 3) case/control:1/0
| | Site: 1 Sens: 1-->0
- \----* 1+(6) case/control:150/144
+ \----* 1+(6) (LEVEL: 2) case/control:150/144
| Site: 3 Sens: 0-->1
- | /----* H012 case/control:1/2
- | |----* H009 case/control:5/10
+ | /----* H012 (LEVEL: 4) case/control:1/2
+ | |----* H009 (LEVEL: 4) case/control:5/10
| | Site: 8 Sens: 0-->1
- \----* 16+(29) case/control:148/139
+ \----* 16+(29) (LEVEL: 3) case/control:148/139
| Site: 6 Sens: 1-->0
- | /----* H002 case/control:9/3
- \----* 8 case/control:142/127
+ | /----* H002 (LEVEL: 5) case/control:9/3
+ \----* 8 (LEVEL: 4) case/control:142/127
| Site: 5 Sens: 0-->1
- | /----* H021 case/control:11/2
+ | /----* H021 (LEVEL: 6) case/control:11/2
| | Site: 8 Sens: 0-->1
- \----* 26 case/control:133/124
+ \----* 26 (LEVEL: 5) case/control:133/124
| Site: 1 Sens: 1-->0
- | /----* H032 case/control:0/1
+ | /----* H032 (LEVEL: 7) case/control:0/1
| | Site: 7 Sens: 0-->1
- | |----* H016 case/control:2/2
- \----* 7+(24) case/control:122/122
+ | |----* H016 (LEVEL: 7) case/control:2/2
+ \----* 7+(24) (LEVEL: 6) case/control:122/122
| Site: 3 Sens: 1-->0
- | /----* H025 case/control:2/3
+ | /----* H025 (LEVEL: 9) case/control:2/3
| | Site: 5 Sens: 1-->0
- | /----* 25 case/control:13/5
+ | /----* 25 (LEVEL: 8) case/control:13/5
| | | Site: 6 Sens: 0-->1
- | | \----* H004 case/control:11/2
- | |----* H008 case/control:28/19
- | |----* H005 case/control:2/2
+ | | \----* H004 (LEVEL: 9) case/control:11/2
+ | |----* H008 (LEVEL: 8) case/control:28/19
+ | |----* H005 (LEVEL: 8) case/control:2/2
| | Site: 10 Sens: 1-->0
- \----* 2+(19+(28+(30))) case/control:120/119
+ \----* 2+(19+(28+(30))) (LEVEL: 7) case/control:120/119
| Site: 4 Sens: 1-->0
- |----* H031 case/control:1/0
+ |----* H031 (LEVEL: 8) case/control:1/0
| Site: 8 Sens: 0-->1
- | /----* H024 case/control:1/0
- \----* 14 case/control:76/93
+ | /----* H024 (LEVEL: 9) case/control:1/0
+ \----* 14 (LEVEL: 8) case/control:76/93
| Site: 9 Sens: 0-->1
- | /----* H013 case/control:15/5
- | /----* 23 case/control:72/90
+ | /----* H013 (LEVEL: 11) case/control:15/5
+ | /----* 23 (LEVEL: 10) case/control:72/90
| | | Site: 10 Sens: 1-->0
- | | | /----* H022 case/control:9/1
- | | \----* 32 case/control:57/85
+ | | | /----* H022 (LEVEL: 12) case/control:9/1
+ | | \----* 32 (LEVEL: 11) case/control:57/85
| | | Site: 6 Sens: 0-->1
- | | | /----* H033 case/control:0/1
- | | | /----* 18 case/control:1/4
+ | | | /----* H033 (LEVEL: 14) case/control:0/1
+ | | | /----* 18 (LEVEL: 13) case/control:1/4
| | | | | Site: 4 Sens: 0-->1
- | | | | \----* H010 case/control:1/3
+ | | | | \----* H010 (LEVEL: 14) case/control:1/3
| | | | Site: 1 Sens: 0-->1
- | | | |----* H034 case/control:1/0
- | | \----* 4+(12) case/control:48/84
+ | | | |----* H034 (LEVEL: 13) case/control:1/0
+ | | \----* 4+(12) (LEVEL: 12) case/control:48/84
| | | Site: 5 Sens: 1-->0
- | | | /----* H029 case/control:1/3
- | | \----* 20 case/control:46/80
+ | | | /----* H029 (LEVEL: 14) case/control:1/3
+ | | \----* 20 (LEVEL: 13) case/control:46/80
| | | Site: 10 Sens: 0-->1
- | | | /----* H018 case/control:2/2
- | | | | /----* H011 case/control:3/8
- | | | | |----* H003 case/control:2/0
+ | | | /----* H018 (LEVEL: 15) case/control:2/2
+ | | | | /----* H011 (LEVEL: 16) case/control:3/8
+ | | | | |----* H003 (LEVEL: 16) case/control:2/0
| | | | | Site: 5 Sens: 0-->1
- | | | |----* 21+(31) case/control:8/21
+ | | | |----* 21+(31) (LEVEL: 15) case/control:8/21
| | | | | Site: 4 Sens: 0-->1
- | | | | | /----* H014 case/control:2/3
+ | | | | | /----* H014 (LEVEL: 17) case/control:2/3
| | | | | | Site: 1 Sens: 1-->0
- | | | | | |----* H017 case/control:0/8
- | | | | \----* 15+(33) case/control:3/13
+ | | | | | |----* H017 (LEVEL: 17) case/control:0/8
+ | | | | \----* 15+(33) (LEVEL: 16) case/control:3/13
| | | | | Site: 3 Sens: 0-->1
- | | | | \----* H027 case/control:1/2
+ | | | | \----* H027 (LEVEL: 17) case/control:1/2
| | | | Site: 6 Sens: 1-->0
| | | | Site: 10 Sens: 1-->0
- | | \----* 5+(34) case/control:45/77
+ | | \----* 5+(34) (LEVEL: 14) case/control:45/77
| | | Site: 1 Sens: 0-->1
- | | | /----* H001 case/control:24/39
- | | | |----* H015 case/control:2/6
+ | | | /----* H001 (LEVEL: 16) case/control:24/39
+ | | | |----* H015 (LEVEL: 16) case/control:2/6
| | | | Site: 9 Sens: 1-->0
- | | \----* 9+(11)+(13) case/control:35/54
+ | | \----* 9+(11)+(13) (LEVEL: 15) case/control:35/54
| | | Site: 2 Sens: 1-->0
- | | |----* H028 case/control:4/0
+ | | |----* H028 (LEVEL: 16) case/control:4/0
| | | Site: 8 Sens: 1-->0
- | | \----* H020 case/control:5/9
+ | | \----* H020 (LEVEL: 16) case/control:5/9
| | Site: 10 Sens: 1-->0
- \----* 3 case/control:75/93
+ \----* 3 (LEVEL: 9) case/control:75/93
| Site: 8 Sens: 0-->1
| Site: 7 Sens: 0-->1
- \----* H019 case/control:3/3
+ \----* H019 (LEVEL: 10) case/control:3/3
Number of permutation: 1
diff --git a/test/phylip/outgroup_present/association/outfile b/test/phylip/outgroup_present/association/outfile
index e2632ca3168ebf692f7d85641279682c39781638..12fb7de27d7a5bdb10371c422d79ac752a3708ca 100644
--- a/test/phylip/outgroup_present/association/outfile
+++ b/test/phylip/outgroup_present/association/outfile
@@ -1,5 +1,5 @@
-Mixed parsimony algorithm, version 3.63
+Mixed parsimony algorithm, version 3.69
Wagner parsimony method
diff --git a/test/phylip/outgroup_present/association/run_altree b/test/phylip/outgroup_present/association/run_altree
index c270004f29ed676c9bd76ca83a2f82614bf26ff5..a17c02b4aeee6315d5f806d5e88842a949a107ca 100755
--- a/test/phylip/outgroup_present/association/run_altree
+++ b/test/phylip/outgroup_present/association/run_altree
@@ -10,6 +10,6 @@ phylip mix
# The outgroup is not removed, so it is not necessary to specify its
# name.
# Analysis on the first tree only
-../../../../altree -i outfile -j nb_cas_controls.txt \
- -a -t SNP -p phylip -r 1 \
+altree -i outfile -j nb_cas_controls.txt \
+ -a -t SNP -p phylip -r 1 --data-qual qualitative \
--tree-to-analyse 1 -o 1_trio_phy.asso