From 12ba00a69bf76e6e3b8c5d619523bec5c96b8505 Mon Sep 17 00:00:00 2001
From: "cmzmasek@gmail.com"
 <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Date: Thu, 21 Aug 2014 19:11:54 +0000
Subject: [PATCH] outdated

---
 forester/aptx/aptx_example_files/bcl_2.xml         |  450 --------------------
 .../aptx_example_files/demo_colors_and_widths.nhx  |   11 -
 forester/aptx/aptx_example_files/demo_custom1.nhx  |    3 -
 forester/aptx/aptx_example_files/demo_custom2.nhx  |    4 -
 4 files changed, 468 deletions(-)
 delete mode 100644 forester/aptx/aptx_example_files/bcl_2.xml
 delete mode 100644 forester/aptx/aptx_example_files/demo_colors_and_widths.nhx
 delete mode 100644 forester/aptx/aptx_example_files/demo_custom1.nhx
 delete mode 100644 forester/aptx/aptx_example_files/demo_custom2.nhx

diff --git a/forester/aptx/aptx_example_files/bcl_2.xml b/forester/aptx/aptx_example_files/bcl_2.xml
deleted file mode 100644
index f83a1b7..0000000
--- a/forester/aptx/aptx_example_files/bcl_2.xml
+++ /dev/null
@@ -1,450 +0,0 @@
-(
-(
-(
-(
-(
-(
-(
-(
-(
-51_CHICK:0.28045,
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-(
-(
-88_CANFA:0.08127,
-115_MOUSE:0.14168)
-:0.0267[39.0],
-(
-74_BOVIN:0.09416,
-9_HUMAN:0.06828)
-:1.0E-5[55.0])
-:0.38418[100.0])
-:0.18828[33.0],
-(
-159_BRARE:0.01275,
-166_BRARE:0.02259)
-:0.35342[100.0])
-:0.24716[35.0],
-(
-52_CHICK:0.27747,
-144_XENLA:0.34644)
-:0.39739[99.0])
-:0.0946[72.0],
-(
-(
-(
-(
-90_CANFA:0.03744,
-12_HUMAN:0.07368)
-:1.0E-5[46.0],
-64_BOVIN:0.05675)
-:0.5126[100.0],
-142_XENLA:0.26292)
-:0.0983[56.0],
-(
-155_BRARE:1.0E-5,
-154_BRARE:1.0E-5)
-:0.34592[99.0])
-:0.51997[100.0])
-:0.68133[99.0],
-(
-125_MOUSE:0.04425,
-(
-95_CANFA:0.09977,
-13_HUMAN:0.07433)
-:0.14928[40.0])
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-:0.22234[58.0],
-(
-(
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-(
-(
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-(
-(
-122_MOUSE:0.10759,
-(
-(
-(
-11_HUMAN:0.02336,
-68_BOVIN:0.24624)
-:0.0243[32.0],
-92_CANFA:1.0E-5)
-:0.01016[40.0],
-46_CHICK:1.06707)
-:0.09256[44.0])
-:0.1765[73.0],
-147_XENLA:0.43513)
-:0.13835[44.0])
-:0.69471[89.0])
-:0.57089[66.0])
-:0.21409500000000004[33.0],
-(
-(
-(
-(
-(
-(
-(
-(
-(
-(
-140_TETNG:0.92309,
-(
-152_XENLA:0.19286,
-(
-(
-(
-(
-0_HUMAN:1.0E-5,
-72_BOVIN:0.0105)
-:1.0E-5[75.0],
-123_MOUSE:0.01053)
-:1.0E-5[93.0],
-97_CANFA:1.0E-5)
-:0.06125[68.0],
-41_CHICK:0.03818)
-:0.0429[35.0])
-:0.07662[43.0])
-:0.00625[55.0],
-(
-(
-(
-132_TETNG:1.0E-5,
-135_TETNG:1.0E-5)
-:0.02241[81.0],
-102_FUGRU:0.00904)
-:0.18878[96.0],
-167_BRARE:0.26949)
-:0.07344[38.0])
-:0.22305[76.0],
-(
-(
-151_XENLA:0.12315,
-(
-126_MOUSE:1.0E-5,
-(
-96_CANFA:1.0E-5,
-(
-8_HUMAN:1.0E-5,
-79_BOVIN:1.0E-5)
-:1.0E-5[100.0])
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-:0.23552[99.0],
-(
-(
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-164_BRARE:0.02901,
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-136_TETNG:0.01045,
-100_FUGRU:1.0E-5)
-:0.06877[100.0])
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-(
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-129_TETNG:6.9E-4,
-104_FUGRU:0.03078)
-:0.05352[97.0],
-(
-128_TETNG:0.36032,
-(
-103_FUGRU:0.24206,
-(
-106_FUGRU:0.04182,
-(
-(
-112_FUGRU:0.03123,
-113_FUGRU:0.09693)
-:0.0141[71.0],
-(
-108_FUGRU:0.01027,
-111_FUGRU:0.01081)
-:0.195[100.0])
-:1.0E-5[77.0])
-:0.09945[65.0])
-:0.24906[100.0])
-:0.23291[95.0])
-:0.17649[84.0])
-:0.20281[86.0],
-(
-149_XENLA:0.32167,
-(
-49_CHICK:0.05537,
-(
-(
-63_BOVIN:0.1324,
-80_BOVIN:0.13424)
-:0.192[99.0],
-(
-57_BOVIN:0.01041,
-(
-117_MOUSE:1.0E-5,
-(
-87_CANFA:1.0E-5,
-1_HUMAN:1.0E-5)
-:0.01043[66.0])
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-:1.0E-5[51.0])
-:0.03275[83.0])
-:0.07846[90.0])
-:0.03668[58.0])
-:0.04974[25.0])
-:0.0375[23.0])
-:0.17228[52.0],
-25_BRAFL:0.4534)
-:0.08093[32.0],
-15_SPHGR:0.68488)
-:0.09782[15.0],
-21_SPHGR:1.05022)
-:0.10632[4.0],
-(
-33_NEMVE:0.482,
-30_NEMVE:0.47217)
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-(
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-165_BRARE:0.30255,
-162_BRARE:0.62996)
-:0.13116[61.0],
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-137_TETNG:0.24501,
-107_FUGRU:0.04204)
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-:0.33029[89.0],
-(
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-42_CHICK:0.29479,
-143_XENLA:0.60398)
-:0.15529[59.0],
-(
-58_BOVIN:0.05604,
-(
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-(
-85_CANFA:0.01109,
-2_HUMAN:0.01103)
-:1.0E-5[42.0],
-124_MOUSE:0.04504)
-:0.02217[78.0],
-73_BOVIN:1.0E-5)
-:1.0E-5[60.0])
-:0.13595[100.0])
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-:0.4495[92.0],
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-45_CHICK:0.17601,
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-91_CANFA:0.10905,
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-118_MOUSE:0.18633,
-127_MOUSE:1.0E-5)
-:0.18193[100.0],
-3_HUMAN:0.04341)
-:0.06948[63.0])
-:0.05702[52.0],
-(
-76_BOVIN:1.0E-5,
-71_BOVIN:1.0E-5)
-:0.09486[100.0])
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-:0.17977[14.0],
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-157_BRARE:0.2958,
-109_FUGRU:0.19527)
-:0.33571[100.0],
-(
-(
-55_BOVIN:0.43001,
-(
-119_MOUSE:0.64738,
-10_HUMAN:0.18995)
-:0.08251[65.0])
-:0.78705[100.0],
-(
-171_CHICK:0.56823,
-141_XENLA:0.57176)
-:0.09353[48.0])
-:0.1832[68.0])
-:0.40777[73.0],
-40_CAEEL:1.20795)
-:0.13006[23.0])
-:0.28685[9.0])
-:0.07066[2.0],
-(
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-23_BRAFL:1.0E-5,
-24_BRAFL:0.08958)
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-26_BRAFL:1.0E-5)
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-(
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-131_TETNG:0.07883)
-:0.22523[100.0],
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-14_SPHGR:0.61862)
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-(
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-35_NEMVE:0.49481,
-38_NEMVE:0.35293)
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-48_CHICK:1.0E-5)
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-98_DROME:0.38195,
-99_DROME:0.30802)
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-22_BRAFL:0.39195,
-18_SPHGR:0.4734)
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-36_NEMVE:0.36151)
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-5_HUMAN:0.01043)
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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
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
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
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]
-- 
1.7.10.2