outdated

diff --git a/forester/aptx/aptx_example_files/bcl_2.xml b/forester/aptx/aptx_example_files/bcl_2.xml
deleted file mode 100644 (file)
index f83a1b7..0000000
--- a/forester/aptx/aptx_example_files/bcl_2.xml
+++ /dev/null
@@ -1,450 +0,0 @@
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diff --git a/forester/aptx/aptx_example_files/demo_colors_and_widths.nhx b/forester/aptx/aptx_example_files/demo_colors_and_widths.nhx
deleted file mode 100644 (file)
index 772be07..0000000
--- a/forester/aptx/aptx_example_files/demo_colors_and_widths.nhx
+++ /dev/null
@@ -1,11 +0,0 @@
-(((((red1:12[&&NHX:C=200.0.0:W=0],red2:12[&&NHX:C=155.0.0:W=1],red3:12[&&NHX:C=55.0.0:W=2],red4:12[&&NHX:C=30.0.0:W=4])red:12[&&NHX:C=255.0.0:W=2],
- (grey1:12[&&NHX:C=100.50.0],grey2:12[&&NHX:C=100.0.40])grey:12[&&NHX:C=100.100.100:W=3],
- (bred:12[&&NHX:C=255.0.0:W=2],bgreen:12[&&NHX:C=0.255.0:W=8])black:12[&&NHX:C=0.0.0:W=4], 
- (green1:12[&&NHX:C=0.50.0],green2:12[&&NHX:C=0.150.0])green:12[&&NHX:C=0.255.0:W=5],
- ((purp11:12[&&NHX:C=200.100.200:W=7],purp12:12[&&NHX:C=155.100.155:W=5])purp1:12[&&NHX:C=200.0.200:W=2],(red:3[&&NHX:C=255.0.0:W=3],((purp11:12[&&NHX:C=200.100.200:W=7],purp12:12[&&NHX:C=155.100.155:W=4])purp1:12[&&NHX:C=200.0.200:W=2],(red:3[&&NHX:C=255.0.0:W=3],green:4[&&NHX:C=0.255.0:W=2])purp2:12[&&NHX:C=155.0.155:W=3])green:4[&&NHX:C=0.255.0:W=2])purp2:12[&&NHX:C=155.0.155:W=3])purp:12[&&NHX:C=255.0.255:W=6],
- (yello1:12[&&NHX:C=200.150.0:W=2],yello2:12[&&NHX:C=155.100.0:W=3],yello3:12[&&NHX:C=155.100.50:W=4])yello:12[&&NHX:C=255.255.0:W=7])red1:12[&&NHX:C=200.0.0:W=2],red2:12[&&NHX:C=155.0.0:W=1],red3:12[&&NHX:C=55.0.0:W=2],red4:12[&&NHX:C=30.0.0:W=4])red:12[&&NHX:C=255.0.0:W=2],
- (grey1:12[&&NHX:C=100.50.0],grey2:12[&&NHX:C=100.0.40])grey:12[&&NHX:C=100.100.100:W=3],
- (bred:12[&&NHX:C=255.0.0:W=2],bgreen:12[&&NHX:C=0.255.0:W=8])black:12[&&NHX:C=0.0.0:W=4], 
- (green1:12[&&NHX:C=0.50.0],green2:12[&&NHX:C=0.150.0])green:12[&&NHX:C=0.255.0:W=5],
- ((purp11:12[&&NHX:C=200.100.200:W=7],purp12:12[&&NHX:C=155.100.155:W=5])purp1:12[&&NHX:C=200.0.200:W=2],(red:3[&&NHX:C=255.0.0:W=3],((purp11:12[&&NHX:C=200.100.200:W=7],purp12:12[&&NHX:C=155.100.155:W=8])purp1:12[&&NHX:C=200.0.200:W=2],(red:3[&&NHX:C=255.0.0:W=3],green:4[&&NHX:C=0.255.0:W=2])purp2:12[&&NHX:C=155.0.155:W=3])green:4[&&NHX:C=0.255.0:W=2])purp2:12[&&NHX:C=155.0.155:W=3])purp:12[&&NHX:C=255.0.255:W=6],
- (yello1:12[&&NHX:C=200.150.0:W=2],yello2:12[&&NHX:C=155.100.0:W=3],yello3:12[&&NHX:C=155.100.50:W=4])yello:12[&&NHX:C=255.255.0:W=7])big:4[&&NHX:C=34.67.97:W=4],black:5[&&NHX:C=0.0.0:W=2])root:12[&&NHX:C=0.255.255:W=7];

diff --git a/forester/aptx/aptx_example_files/demo_custom1.nhx b/forester/aptx/aptx_example_files/demo_custom1.nhx
deleted file mode 100644 (file)
index b1eacf7..0000000
--- a/forester/aptx/aptx_example_files/demo_custom1.nhx
+++ /dev/null
@@ -1,3 +0,0 @@
-((geneA:12[&&NHX:S=Mouse   :E=1.1.1.1:C=255.12.255:W=2:XN=L=population=200:XN=D=av=20=g],
-  geneB:23[&&NHX:S=Gorilla :E=1.1.1.1:C=255.255.0 :W=3:XN=L=population=300:XN=D=av=800=lb])ab:12[&&NHX:B=95:D=Y:C=123.56.34:C=34.34.56:W=5:XN=L=population=500],
-  geneC:40[&&NHX:S=Bat     :E=1.1.1.1:C=0.255.255 :W=2:XN=L=population=200:XN=D=av=40=g])abc[&&NHX:C=255.0.0:W=7:XN=L=population=700];

diff --git a/forester/aptx/aptx_example_files/demo_custom2.nhx b/forester/aptx/aptx_example_files/demo_custom2.nhx
deleted file mode 100644 (file)
index e2cf372..0000000
--- a/forester/aptx/aptx_example_files/demo_custom2.nhx
+++ /dev/null
@@ -1,4 +0,0 @@
-((((A:0.54[&&NHX:S=seahorse:XN=S=status=doubtful:XN=D=genome=12.3=MB],B:0.28[&&NHX:S=seahorse:XN=S=status=certain:XN=D=genome=11.3=MB])AB:0.93[&&NHX:D=Y],
-(C:0.67[&&NHX:S=emu:XN=S=status=unlikely:XN=D=genome=3.3=MB],D:0.23[&&NHX:S=turtle:XN=S=status=doubtful:XN=D=genome=2.2=MB])CD:0.3[&&NHX:D=N])ABCD:0.4[&&NHX:D=Y],
-E:0.8[&&NHX:S=alligator:XN=S=status=certain:XN=D=genome=4.2=MB])ABCDE:0.56[&&NHX:D=Y],
-F:0.9[&&NHX:S=alligatot:XN=S=status=certain:XN=D=genome=4.3=MB])ABCDEF:0.43[&&NHX:D=Y]