diff --git a/tests/data/InfB_HAt_ALLs1.mcc.tree b/tests/data/InfB_HAt_ALLs1.mcc.tree deleted file mode 100644 index 934ea7b..0000000 --- a/tests/data/InfB_HAt_ALLs1.mcc.tree +++ /dev/null @@ -1,917 +0,0 @@ -#NEXUS - -Begin taxa; - Dimensions ntax=452; - Taxlabels - B/Aichi/1/93_1993 - B/Aichi/5/88_1988 - B/Akita/27/2001_2001 - B/Alaska/03/1992_1992-06-13 - B/Alaska/12/96_1996-10-28 - B/Alaska/16/2000_2000-11-22 - B/Anhui-Huashan/1216/2011_2011-05-10 - B/Anhui-Luyang/1142/2011_2011-05-03 - B/Ann_Arbor/1/1986_1986 - B/Ann_Arbor/1994_1994 - B/Argentina/132/2001_2001-08-07 - B/Argentina/3640/1999_1999 - B/Auckland/01/2000_2000-05-09 - B/Bangkok/141/1994_1994-05-07 - B/Bangkok/153/1990_1990 - B/Bangkok/163/1990_1990 - B/Bangkok/460/03_2003 - B/Bangladesh/1994/2010_2010-01-20 - B/Bangladesh/3333/2007_2007 - B/Bangladesh/5945/2009_2009-09-30 - B/Bangladesh/9673/2009_2009-11-01 - B/Barcelona/215/03_2003 - B/Beijing-Huairou/1338/2011_2011-03-10 - B/Beijing-Xicheng/11082/2010_2010-05-04 - B/Beijing-Xicheng/1267/2011_2011-02-27 - B/Beijing-Xicheng/1291/2011_2011-03-09 - B/Beijing-Xicheng/1677/2011_2011-04-06 - B/Beijing-Xicheng/1846/2010_2010-04-06 - B/Beijing-Xicheng/1875/2011_2011-05-03 - B/Beijing-Xicheng/1962/2011_2011-05-23 - B/Beijing/184/93_1993 - B/Beijing/243/97_1997 - B/Beijing/76/98_1998 - B/Bolivia/104/2010_2010-03-19 - B/Boston/DB02/2011_2011-03-18 - B/Brazil/975/2000_2000-06-09 - B/Brisbane/32/2002_2002 - B/Brisbane/33/2008_2008-07-13 - B/Brisbane/60-1/2010_2010-10-07 - B/Brisbane/60-12/2010_2010-10-09 - B/Brisbane/60-2/2010_2010-11-09 - B/Brisbane/60-3/2010_2010-11-23 - B/Brisbane/60-4/2010_2010-10-09 - B/Brisbane/60-5/2010_2010-12-01 - B/Brisbane/60-6/2010_2010-09-13 - B/Brisbane/60-7/2010_2010-09-15 - B/Brisbane/60/2008_2008-08-04 - B/Bucharest/311/1998_1998 - B/Bucharest/795/03_2003 - B/California/01/1995_1995 - B/California/02/1994_1994-12-13 - B/California/02/1995_1995-02-16 - B/California/NHRC0001/2005_2005-01-25 - B/California/NHRC0001/2006_2006-03-29 - B/California/NHRC0002/2005_2005-01-25 - B/California/NHRC0002/2006_2006-03-09 - B/California/NHRC0003/2005_2005-01-26 - B/California/NHRC0004/2003_2003-03-06 - B/California/NHRC0004/2005_2005-01-27 - B/California/NHRC0004/2006_2006-02-28 - B/California/NHRC0005/2003_2003-03-10 - B/California/NHRC0005/2005_2005-01-18 - B/California/NHRC0005/2006_2006-02-28 - B/California/NHRC0006/2005_2005-01-21 - B/California/NHRC0008/2005_2005-02-22 - B/Cambodia/30/2011_2011-01-04 - B/Canada/16188/2000_2000-11-23 - B/Chantaburi/218/2003_2003-07-26 - B/Cheju/303/03_2003 - B/Cheongju/411/2008_2008-02-19 - B/Cheongju/437/2008_2008-02-23 - B/Chiba/447/98_1998 - B/Chile/3162/2002_2002-03-14 - B/Chongqing-Jiulongpo/39/2011_2011-04-12 - B/Chongqing-Wanzhou/1152/2011_2011-03-08 - B/Chongqing-Wanzhou/1162/2011_2011-03-15 - B/Chongqing-Wanzhou/1294/2011_2011-06-18 - B/Chongqing-Wanzhou/145/2011_2011-02-03 - B/Chongqing-Yuzhong/1294/2010_2010-05-05 - B/Colorado/04/2004_2004-11-09 - B/Colorado/13/2004_2004-12-14 - B/Connecticut/02/1995_1995-01-05 - B/Connecticut/07/1993_1993-01-26 - B/Cordoba/2979/1991_1991-06-13 - B/Czechoslovakia/69/1990_1990 - B/Egypt/2040/2004_2004-04-27 - B/Finland/39/2010_2010-12-30 - B/Florida/02/1998_1998-11-11 - B/Florida/02/2006_2006-01-09 - B/Florida/4/2006_2006 - B/Florida/7/2004_2004 - B/Florida/UR06-0001/2006_2006-11-13 - B/Florida/UR06-0002/2006_2006-11-15 - B/Florida/UR06-0003/2006_2006-11-16 - B/Florida/UR06-0006/2006_2006-11-27 - B/Fujian-Cangshan/1194/2010_2010-05-10 - B/Fujian-Cangshan/192/2011_2011-02-27 - B/Fujian-Gulou/1174/2011_2011-03-09 - B/Fujian-Gulou/1272/2008_2008 - B/Fujian-Gulou/1553/2011_2011-08-31 - B/Fujian-Licheng/118/2010_2010-07-09 - B/Fujian-Meilie/1440/2010_2010-08-19 - B/Fujian-Xiangcheng/2150/2011_2011-05-30 - B/Fujian-Xianyou/137/2011_2011-02-18 - B/Gansu-Chengguan/572/2011_2011-03-10 - B/Geneva/5079/03_2003 - B/Georgia/01/2011_2011-01-01 - B/Georgia/02/1998_1998-11-28 - B/Georgia/04/1998_1998 - B/Georgia/09/2005_2005-02-14 - B/Georgia/NHRC0001/2001_2001-01-09 - B/Georgia/NHRC0001/2003_2003-01-16 - B/Georgia/NHRC0001/2006_2006-05-29 - B/Guangdong-Chikan/1155/2011_2011-05-03 - B/Guangdong-Chikan/1370/2010_2010-07-26 - B/Guangdong-Dongguanbendi/1721/2010_2010-09-01 - B/Guangdong-Huicheng/1235/2011_2011-06-01 - B/Guangdong-Luohu/1512/2010_2010-06-21 - B/Guangxi-Xixiangtang/1455/2010_2010-06-18 - B/Guangxi-Xixiangtang/1545/2010_2010-08-16 - B/Guangzhou/01/2007_2007-07-12 - B/Guatemala/52/2012_2012-02-19 - B/Guizhou-Nanming/1443/2010_2010-06-07 - B/HONG_KONG/2196/2010_2010-11-30 - B/Harbin/7/1994_1994 - B/Hawaii/10/2001_2001-05-09 - B/Hawaii/11/2004_2004-06-14 - B/Hawaii/13/2004_2004-06-21 - B/Hawaii/33/2004_2004 - B/Heilongjiang-Gongnong/182/2011_2011-02-16 - B/Henan/22/97_1997 - B/Hong_Kong/02/1993_1993-02-15 - B/Hong_Kong/03/1992_1992-03-23 - B/Hong_Kong/06/2001_2001-01-08 - B/Hong_Kong/1115/2002_2002-01-15 - B/Hong_Kong/123/2001_2001-02-23 - B/Hong_Kong/1351/02_2002-01-17 - B/Hong_Kong/1434/2002_2002-01-18 - B/Hong_Kong/167/2002_2002-01-03 - B/Hong_Kong/22/1989_1989 - B/Hong_Kong/22/2001_2001-01-18 - B/Hong_Kong/28/2001_2001-01-22 - B/Hong_Kong/293/02_2002 - B/Hong_Kong/310/2004_2004-11-24 - B/Hong_Kong/330/2001_2001 - B/Hong_Kong/542/2000_2000-07-20 - B/Hong_Kong/553a/2003_2003-03-31 - B/Hong_Kong/557/2000_2000-10-04 - B/Hong_Kong/70/1996_1996 - B/Houston/1/91_1991 - B/Houston/B15/1999_1999-02-12 - B/Houston/B56/1997_1997-01-27 - B/Houston/B57/1997_1997-02-10 - B/Houston/B60/1997_1997-02-25 - B/Houston/B63/1997_1997-03-05 - B/Houston/B65/1998_1998-05-04 - B/Houston/B66/2000_2000-03-10 - B/Houston/B67/2000_2000-03-22 - B/Houston/B68/2000_2000-04-16 - B/Houston/B69/2002_2002-03-21 - B/Houston/B71/2002_2002-02-23 - B/Houston/B720/2004_2004-12-28 - B/Houston/B74/2002_2002-03-18 - B/Houston/B745/2005_2005-01-03 - B/Houston/B75/2002_2002-03-20 - B/Houston/B756/2005_2005-01-04 - B/Houston/B77/2002_2002-03-21 - B/Houston/B787/2005_2005-01-06 - B/Houston/B79/2003_2003 - B/Houston/B81/2003_2003-01-16 - B/Houston/B84/2003_2003-01-15 - B/Houston/B846/2005_2005-01-12 - B/Houston/B850/2005_2005-01-12 - B/Houston/B86/2003_2003-01-21 - B/Houston/B87/2003_2003-01-19 - B/Houston/B88/2003_2003-01-17 - B/Hubei-Wuchang/1108/2011_2011-04-03 - B/Hubei-Wujiagang/1112/2010_2010-08-27 - B/Hubei-Wujiagang/158/2009_2009 - B/Hunan-Beihu/1300/2011_2011-05-26 - B/Hunan-Hecheng/1104/2011_2011-03-15 - B/Hunan-Hengnan/35/2011_2011-06-29 - B/Hunan-Louxing/160/2011_2011-03-14 - B/Hunan-Lusong/1126/2011_2011-02-16 - B/Hunan-Lusong/1325/2011_2011-05-11 - B/Hunan-Suxian/54/2011_2011-04-10 - B/Hunan-Suxian/56/2011_2011-04-11 - B/Hunan-Yuhu/134/2011_2011-03-02 - B/Hunan-Yuhua/11100/2010_2010-09-08 - B/Hunan-Yuhua/1265/2011_2011-05-03 - B/Hunan-Yuhua/1316/2011_2011-06-02 - B/Ibaraki/2/85_1985 - B/Illinois/13/2005_2005-02-03 - B/Illinois/47/2005_2005-03-07 - B/Illinois/NHRC0001/2003_2003-02-24 - B/Illinois/NHRC0001/2006_2006-02-22 - B/Illinois/UR06-0016/2007_2007-01-02 - B/Illinois/UR06-0516/2007_2007-03-05 - B/Indiana/01/1995_1995 - B/Iowa/03/2002_2002-03-19 - B/Israel/95/03_2003 - B/Jiangsu-Beitang/1135/2011_2011-04-05 - B/Jiangsu-Beitang/1141/2011_2011-04-07 - B/Jiangsu-Chongchuan/11150/2011_2011-06-27 - B/Jiangsu-Nanjinggulou/1655/2011_2011-05-20 - B/Jiangsu-Pizhou/529/2011_2011-04-25 - B/Jiangsu-Quanshan/1329/2011_2011-04-27 - B/Jiangsu-Xinpu/192/2011_2011-03-02 - B/Jiangxi-Donghu/1329/2010_2010-04-01 - B/Jilin/20/2003_2003 - B/Johannesburg/05/1999_1999 - B/Johannesburg/06/1994_1994 - B/Johannesburg/69/2001_2001-06-12 - B/Kouchi/193/99_1999-02-02 - B/Laos/89/2011_2011-02-21 - B/Lisbon/02/1994_1994-10-26 - B/Los_Angeles/1/02_2002 - B/Maine/05/2011_2011-03-08 - B/Malaysia/2506/2004_2004 - 'B/Managua/1312.01/2010_2010-07-03' - 'B/Managua/1361.01/2010_2010-07-22' - 'B/Managua/1499.02/2010_2010-10-05' - 'B/Managua/1504.03/2010_2010-08-20' - 'B/Managua/164.02/2010_2010-07-26' - 'B/Managua/1873.01/2010_2010-06-15' - 'B/Managua/2037.01/2010_2010-08-28' - 'B/Managua/2090.02/2010_2010-07-15' - 'B/Managua/2630.01/2010_2010-08-29' - 'B/Managua/2826.02/2010_2010-08-11' - 'B/Managua/3323.01/2010_2010-08-25' - 'B/Managua/3759.01/2008_2008-06-04' - 'B/Managua/4403.06/2010_2010-09-02' - 'B/Managua/4437.01/2010_2010-10-02' - 'B/Managua/4468.03/2010_2010-10-11' - 'B/Managua/4485.05/2010_2010-08-10' - 'B/Managua/4577.01/2008_2008-06-02' - 'B/Managua/4705.02/2008_2008-04-21' - 'B/Managua/4772.01/2010_2010-10-08' - 'B/Managua/4787.01/2008_2008-03-04' - 'B/Managua/4834.02/2010_2010-08-03' - 'B/Managua/4847.02/2008_2008-05-27' - 'B/Managua/4942.04/2010_2010-09-17' - 'B/Managua/5227.05/2010_2010-08-31' - 'B/Managua/5454.02/2010_2010-07-04' - 'B/Managua/5549.04/2010_2010-09-17' - 'B/Managua/5590.04/2010_2010-06-04' - 'B/Managua/5839.01/2010_2010-09-04' - 'B/Managua/6006.03/2010_2010-08-05' - B/Maryland/1/01_2001 - B/Memphis/12/97_1997 - B/Memphis/13/03_2003 - B/Memphis/3/89_1989 - B/Memphis/5/93_1993 - B/Mexico/84/2000_2000-03-10 - B/Michigan/01/2009_2009-04-04 - B/Michigan/04/2006_2006-04-04 - B/Mie/01/1993_1993 - B/Mississippi/UR06-0031/2007_2007-01-16 - B/Mississippi/UR06-0317/2007_2007-02-15 - B/Mississippi/UR06-0340/2007_2007-02-19 - B/Mississippi/UR06-0348/2007_2007-02-20 - B/Mississippi/UR06-0409/2007_2007-02-23 - B/Mississippi/UR06-0446/2007_2007-02-27 - B/Mississippi/UR06-0477/2007_2007-03-01 - B/Mississippi/UR06-0492/2007_2007-03-02 - B/Mississippi/UR06-0551/2007_2007-03-08 - B/Missouri/03/2011_2011-03-01 - B/Missouri/NHRC0001/2001_2001-01-19 - B/Missouri/NHRC0001/2003_2003-03-04 - B/Moscow/16/2002_2002-02-22 - B/Moscow/3/03_2003 - B/Nanchang/2/97_1997 - B/Nanchang/6/96_1996 - B/Nanchang/6/98_1998 - B/Nanchang/630/94_1994 - B/Nebraska/1/01_2001 - B/Nebraska/2/01_2001 - B/Nepal/1331/2005_2005-07-13 - B/Nevada/03/2011_2011-02-02 - B/Nevada/11/2011_2011-03-14 - B/Nevada/12/2011_2011-03-14 - B/New_Jersey/NHRC0001/2005_2005-05-16 - B/New_York/24/1993_1993-12-08 - B/New_York/347/1999_1999-01-19 - B/New_York/39/1991_1991-03-20 - B/North_Carolina/03/2011_2011-01-05 - B/North_Carolina/04/2011_2011-01-26 - B/North_Carolina/18/2011_2011-02-07 - B/North_Carolina/20/2011_2011-01-06 - B/North_Carolina/22/2011_2011-01-13 - B/North_Carolina/23/2011_2011-02-18 - B/North_Carolina/WRAIR1582P/2009_2009-03 - B/Norway/1/84_1984 - B/Norway/24/2011_2011-01-04 - B/Ohio/01/2005_2005-02-23 - B/Ohio/UR06-0410/2007_2007-02-23 - B/Ohio/UR06-0428/2007_2007-02-26 - B/Ohio/UR06-0572/2007_2007-03-12 - B/Oita/15/92_1992-10-16 - B/Osaka/547/1997_1997 - B/PHILIPPINES/2533/2011_2011-07-27 - B/PHILIPPINES/3701/2011_2011-10-06 - B/Panama/307237/2010_2010-06-22 - B/Panama/45/90_1990 - B/Paraguay/636/2003_2003-12-13 - B/Paris/549/1999_1999 - B/Pennsylvania/PIT59/2008_2008-03-15 - B/Pennsylvania/PIT63/2008_2008-03-20 - B/Pennsylvania/PIT66/2008_2008-03-05 - B/Perth/25/2002_2002-07-09 - B/Romania/217/1999_1999-02-08 - B/Romania/318/1998_1998-04-06 - B/Russia/22/1995_1995 - B/SYDNEY/508/2010_2010-10-11 - B/Shaanxi-Beilin/1165/2011_2011-02-15 - B/Shaanxi-Beilin/1230/2011_2011-03-02 - B/Shangdong/7/97_1997 - B/Shanghai-Baoshan/152/2011_2011-02-09 - B/Shanghai-Baoshan/193/2011_2011-03-07 - B/Shanghai-Baoshan/197/2011_2011-03-07 - B/Shanghai-Chongming/1411/2010_2010-07-12 - B/Shanghai-Fengxian/1550/2010_2010-09-05 - B/Shanghai-Hongkou/1255/2011_2011-05-06 - B/Shanghai-Huangpu/171/2011_2011-02-22 - B/Shanghai-Jingan/1392/2011_2011-04-18 - B/Shanghai-Luwan/1135/2011_2011-03-13 - B/Shanghai-Luwan/1169/2011_2011-04-05 - B/Shanghai-Luwan/1188/2011_2011-04-12 - B/Shanghai-Luwan/1217/2011_2011-05-04 - B/Shanghai-Luwan/187/2011_2011-02-15 - B/Shanghai-Pudongxin/1238/2011_2011-05-13 - B/Shanghai-Pudongxin/1467/2010_2010-05-05 - B/Shanghai-Songjiang/1108/2011_2011-03-02 - B/Shanghai-Songjiang/1204/2011_2011-05-04 - B/Shanghai-Songjiang/176/2011_2011-02-10 - B/Shanghai-Zhangning/1133/2011_2011-02-24 - B/Shanghai-Zhangning/1143/2011_2011-03-01 - B/Shanghai-Zhangning/1423/2010_2010-06-11 - B/Shiga/51/98_1998 - B/Shiga/T30/98_1998 - B/Shizuoka/15/2001_2001 - B/Shizuoka/480/2000_2000 - B/Sichuan-Anyue/139/2011_2011-03-02 - B/Sichuan-Jinjiang/277/2011_2011-03-16 - B/Sichuan-Qingyang/1305/2010_2010-07-11 - B/Sichuan-Wenjiang/279/2011_2011-05-04 - B/Sichuan-Yucheng/1212/2011_2011-04-03 - B/Sichuan/379/99_1999 - B/Singapore/04/1991_1991-07-10 - B/Singapore/11/94_1994-05-10 - B/Singapore/22/1998_1998 - B/Singapore/31/1998_1998 - B/Singapore/35/1998_1998-10-22 - B/South_Carolina/04/2003_2003-02-06 - B/South_Carolina/NHRC0001/2000_2000-02-14 - B/South_Carolina/NHRC0001/2001_2001-01-17 - B/South_Carolina/NHRC0001/2004_2004-12-23 - B/South_Carolina/NHRC0001/2005_2005-02-15 - B/South_Carolina/NHRC0002/2001_2001-01-30 - 'B/St._Petersburg/14/2006_2006-03-14' - B/Taiwan/11/2010_2010-04-06 - B/Taiwan/1197/94_1994-05-12 - B/Taiwan/125/2004_2004-02-10 - B/Taiwan/1484/2001_2001-05-25 - B/Taiwan/1734/2006_2006-12-22 - B/Taiwan/1838/2006_2006-12-30 - B/Taiwan/202/2005_2005 - B/Taiwan/2171/2004_2004 - B/Taiwan/2643/2002_2002-05-21 - B/Taiwan/2755/2006_2006-11-11 - B/Taiwan/2894/2006_2006-11-23 - B/Taiwan/3001/2006_2006-11-30 - B/Taiwan/3246/2002_2002-06-13 - B/Taiwan/3395/2004_2004-12-31 - B/Taiwan/37/2007_2007-01-12 - B/Taiwan/383/2005_2005-01-27 - B/Taiwan/40/2007_2007-01-13 - B/Taiwan/417/2005_2005-01-28 - B/Taiwan/42/2007_2007-01-16 - B/Taiwan/45/2001_2001-01-03 - B/Taiwan/45/2007_2007-01-03 - B/Taiwan/481/2001_2001-02-15 - B/Taiwan/500/2005_2005 - B/Taiwan/539/2005_2005-02-07 - B/Taiwan/634/2001_2001-02-28 - B/Taiwan/70028/2007_2007-01-04 - B/Taiwan/70061/2006_2006-01-16 - B/Taiwan/70690/2006_2006-05-12 - B/Taiwan/71523/2007_2007-08-06 - B/Taiwan/72068/2004_2004-12-02 - B/Taiwan/783/2005_2005-03-23 - B/Taiwan/91061/2005_2005-11-16 - B/Taiwan/94/2005_2005-01-10 - B/Tehran/80/02_2002 - B/Temple/B10/1999_1999-02-10 - B/Temple/B1166/2001_2001 - B/Temple/B1181/2001_2001 - B/Temple/B1182/2001_2001 - B/Temple/B1188/2001_2001 - B/Temple/B1190/2001_2001 - B/Temple/B1193/2001_2001 - B/Temple/B17/2003_2003 - B/Temple/B18/2003_2003 - B/Temple/B19/2003_2003 - B/Temple/B20/2003_2003 - B/Temple/B21/2003_2003 - B/Temple/B24/2003_2003 - B/Temple/B3/1999_1999-02-09 - B/Temple/B30/2003_2003 - B/Temple/B7/1999_1999-02-11 - B/Temple/B8/1999_1999-02-05 - B/Temple/B9/1999_1999-02-09 - B/Tennessee/UR06-0079/2007_2007-01-26 - B/Tennessee/UR06-0105/2007_2007-01-29 - B/Tennessee/UR06-0261/2007_2007-02-13 - B/Tennessee/UR06-0310/2007_2007-02-15 - B/Tennessee/UR06-0320/2007_2007-02-15 - B/Tennessee/UR06-0407/2007_2007-02-23 - B/Tennessee/UR06-0431/2007_2007-02-26 - B/Tennessee/UR06-0460/2007_2007-02-27 - B/Tennessee/UR06-0559/2007_2007-03-08 - B/Texas/06/2000_2000-05-03 - B/Texas/06/2011_2011-02-16 - B/Texas/07/2011_2011-03-04 - B/Texas/14/1991_1991-01-11 - B/Texas/37/1988_1988 - B/Texas/NHRC0001/2005_2005-04-08 - B/Texas/NHRC0001/2006_2006-04-05 - B/Texas/UR06-0343/2007_2007-02-19 - B/Texas/UR06-0541/2007_2007-03-06 - B/Texas/UR06-0590/2007_2007-03-13 - B/Tianjin-Binhaixin/1125/2011_2011-04-12 - B/Tianjin-Hedong/1174/2011_2011-05-15 - B/Tianjin-Hexi/1112/2011_2011-03-18 - B/Tianjin-Hexi/156/2011_2011-02-15 - B/Tianjin-Hexi/180/2011_2011-02-28 - B/Ulan-Ude/6/2003_2003-03-06 - B/Utah/03/2011_2011-02-21 - B/VICTORIA/304/2006_2006-06-06 - B/VICTORIA/500/2012_2012-02-26 - B/Victoria/02/1987_1987 - B/Victoria/504/2000_2000-08-03 - B/Vietnam/92/2011_2011-03-22 - B/Virginia/01/2011_2011-01-25 - B/Virginia/03/2011_2011-02-16 - B/Virginia/04/2011_2011-01-31 - B/Virginia/05/2011_2011-02-04 - B/Washington/04/2011_2011-03-04 - B/Wellington/01/1994_1994 - B/Wisconsin/03/2012_2012 - B/Yamagata/16/88_1988 - B/Yamanashi/166/98_1998 - ; -End; - -Begin trees; - Translate - 1 B/Aichi/1/93_1993, - 2 B/Aichi/5/88_1988, - 3 B/Akita/27/2001_2001, - 4 B/Alaska/03/1992_1992-06-13, - 5 B/Alaska/12/96_1996-10-28, - 6 B/Alaska/16/2000_2000-11-22, - 7 B/Anhui-Huashan/1216/2011_2011-05-10, - 8 B/Anhui-Luyang/1142/2011_2011-05-03, - 9 B/Ann_Arbor/1/1986_1986, - 10 B/Ann_Arbor/1994_1994, - 11 B/Argentina/132/2001_2001-08-07, - 12 B/Argentina/3640/1999_1999, - 13 B/Auckland/01/2000_2000-05-09, - 14 B/Bangkok/141/1994_1994-05-07, - 15 B/Bangkok/153/1990_1990, - 16 B/Bangkok/163/1990_1990, - 17 B/Bangkok/460/03_2003, - 18 B/Bangladesh/1994/2010_2010-01-20, - 19 B/Bangladesh/3333/2007_2007, - 20 B/Bangladesh/5945/2009_2009-09-30, - 21 B/Bangladesh/9673/2009_2009-11-01, - 22 B/Barcelona/215/03_2003, - 23 B/Beijing-Huairou/1338/2011_2011-03-10, - 24 B/Beijing-Xicheng/11082/2010_2010-05-04, - 25 B/Beijing-Xicheng/1267/2011_2011-02-27, - 26 B/Beijing-Xicheng/1291/2011_2011-03-09, - 27 B/Beijing-Xicheng/1677/2011_2011-04-06, - 28 B/Beijing-Xicheng/1846/2010_2010-04-06, - 29 B/Beijing-Xicheng/1875/2011_2011-05-03, - 30 B/Beijing-Xicheng/1962/2011_2011-05-23, - 31 B/Beijing/184/93_1993, - 32 B/Beijing/243/97_1997, - 33 B/Beijing/76/98_1998, - 34 B/Bolivia/104/2010_2010-03-19, - 35 B/Boston/DB02/2011_2011-03-18, - 36 B/Brazil/975/2000_2000-06-09, - 37 B/Brisbane/32/2002_2002, - 38 B/Brisbane/33/2008_2008-07-13, - 39 B/Brisbane/60-1/2010_2010-10-07, - 40 B/Brisbane/60-12/2010_2010-10-09, - 41 B/Brisbane/60-2/2010_2010-11-09, - 42 B/Brisbane/60-3/2010_2010-11-23, - 43 B/Brisbane/60-4/2010_2010-10-09, - 44 B/Brisbane/60-5/2010_2010-12-01, - 45 B/Brisbane/60-6/2010_2010-09-13, - 46 B/Brisbane/60-7/2010_2010-09-15, - 47 B/Brisbane/60/2008_2008-08-04, - 48 B/Bucharest/311/1998_1998, - 49 B/Bucharest/795/03_2003, - 50 B/California/01/1995_1995, - 51 B/California/02/1994_1994-12-13, - 52 B/California/02/1995_1995-02-16, - 53 B/California/NHRC0001/2005_2005-01-25, - 54 B/California/NHRC0001/2006_2006-03-29, - 55 B/California/NHRC0002/2005_2005-01-25, - 56 B/California/NHRC0002/2006_2006-03-09, - 57 B/California/NHRC0003/2005_2005-01-26, - 58 B/California/NHRC0004/2003_2003-03-06, - 59 B/California/NHRC0004/2005_2005-01-27, - 60 B/California/NHRC0004/2006_2006-02-28, - 61 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B/Hong_Kong/1115/2002_2002-01-15, - 136 B/Hong_Kong/123/2001_2001-02-23, - 137 B/Hong_Kong/1351/02_2002-01-17, - 138 B/Hong_Kong/1434/2002_2002-01-18, - 139 B/Hong_Kong/167/2002_2002-01-03, - 140 B/Hong_Kong/22/1989_1989, - 141 B/Hong_Kong/22/2001_2001-01-18, - 142 B/Hong_Kong/28/2001_2001-01-22, - 143 B/Hong_Kong/293/02_2002, - 144 B/Hong_Kong/310/2004_2004-11-24, - 145 B/Hong_Kong/330/2001_2001, - 146 B/Hong_Kong/542/2000_2000-07-20, - 147 B/Hong_Kong/553a/2003_2003-03-31, - 148 B/Hong_Kong/557/2000_2000-10-04, - 149 B/Hong_Kong/70/1996_1996, - 150 B/Houston/1/91_1991, - 151 B/Houston/B15/1999_1999-02-12, - 152 B/Houston/B56/1997_1997-01-27, - 153 B/Houston/B57/1997_1997-02-10, - 154 B/Houston/B60/1997_1997-02-25, - 155 B/Houston/B63/1997_1997-03-05, - 156 B/Houston/B65/1998_1998-05-04, - 157 B/Houston/B66/2000_2000-03-10, - 158 B/Houston/B67/2000_2000-03-22, - 159 B/Houston/B68/2000_2000-04-16, - 160 B/Houston/B69/2002_2002-03-21, - 161 B/Houston/B71/2002_2002-02-23, - 162 B/Houston/B720/2004_2004-12-28, - 163 B/Houston/B74/2002_2002-03-18, - 164 B/Houston/B745/2005_2005-01-03, - 165 B/Houston/B75/2002_2002-03-20, - 166 B/Houston/B756/2005_2005-01-04, - 167 B/Houston/B77/2002_2002-03-21, - 168 B/Houston/B787/2005_2005-01-06, - 169 B/Houston/B79/2003_2003, - 170 B/Houston/B81/2003_2003-01-16, - 171 B/Houston/B84/2003_2003-01-15, - 172 B/Houston/B846/2005_2005-01-12, - 173 B/Houston/B850/2005_2005-01-12, - 174 B/Houston/B86/2003_2003-01-21, - 175 B/Houston/B87/2003_2003-01-19, - 176 B/Houston/B88/2003_2003-01-17, - 177 B/Hubei-Wuchang/1108/2011_2011-04-03, - 178 B/Hubei-Wujiagang/1112/2010_2010-08-27, - 179 B/Hubei-Wujiagang/158/2009_2009, - 180 B/Hunan-Beihu/1300/2011_2011-05-26, - 181 B/Hunan-Hecheng/1104/2011_2011-03-15, - 182 B/Hunan-Hengnan/35/2011_2011-06-29, - 183 B/Hunan-Louxing/160/2011_2011-03-14, - 184 B/Hunan-Lusong/1126/2011_2011-02-16, - 185 B/Hunan-Lusong/1325/2011_2011-05-11, - 186 B/Hunan-Suxian/54/2011_2011-04-10, - 187 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'B/Managua/4577.01/2008_2008-06-02', - 237 'B/Managua/4705.02/2008_2008-04-21', - 238 'B/Managua/4772.01/2010_2010-10-08', - 239 'B/Managua/4787.01/2008_2008-03-04', - 240 'B/Managua/4834.02/2010_2010-08-03', - 241 'B/Managua/4847.02/2008_2008-05-27', - 242 'B/Managua/4942.04/2010_2010-09-17', - 243 'B/Managua/5227.05/2010_2010-08-31', - 244 'B/Managua/5454.02/2010_2010-07-04', - 245 'B/Managua/5549.04/2010_2010-09-17', - 246 'B/Managua/5590.04/2010_2010-06-04', - 247 'B/Managua/5839.01/2010_2010-09-04', - 248 'B/Managua/6006.03/2010_2010-08-05', - 249 B/Maryland/1/01_2001, - 250 B/Memphis/12/97_1997, - 251 B/Memphis/13/03_2003, - 252 B/Memphis/3/89_1989, - 253 B/Memphis/5/93_1993, - 254 B/Mexico/84/2000_2000-03-10, - 255 B/Michigan/01/2009_2009-04-04, - 256 B/Michigan/04/2006_2006-04-04, - 257 B/Mie/01/1993_1993, - 258 B/Mississippi/UR06-0031/2007_2007-01-16, - 259 B/Mississippi/UR06-0317/2007_2007-02-15, - 260 B/Mississippi/UR06-0340/2007_2007-02-19, - 261 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B/Russia/22/1995_1995, - 314 B/SYDNEY/508/2010_2010-10-11, - 315 B/Shaanxi-Beilin/1165/2011_2011-02-15, - 316 B/Shaanxi-Beilin/1230/2011_2011-03-02, - 317 B/Shangdong/7/97_1997, - 318 B/Shanghai-Baoshan/152/2011_2011-02-09, - 319 B/Shanghai-Baoshan/193/2011_2011-03-07, - 320 B/Shanghai-Baoshan/197/2011_2011-03-07, - 321 B/Shanghai-Chongming/1411/2010_2010-07-12, - 322 B/Shanghai-Fengxian/1550/2010_2010-09-05, - 323 B/Shanghai-Hongkou/1255/2011_2011-05-06, - 324 B/Shanghai-Huangpu/171/2011_2011-02-22, - 325 B/Shanghai-Jingan/1392/2011_2011-04-18, - 326 B/Shanghai-Luwan/1135/2011_2011-03-13, - 327 B/Shanghai-Luwan/1169/2011_2011-04-05, - 328 B/Shanghai-Luwan/1188/2011_2011-04-12, - 329 B/Shanghai-Luwan/1217/2011_2011-05-04, - 330 B/Shanghai-Luwan/187/2011_2011-02-15, - 331 B/Shanghai-Pudongxin/1238/2011_2011-05-13, - 332 B/Shanghai-Pudongxin/1467/2010_2010-05-05, - 333 B/Shanghai-Songjiang/1108/2011_2011-03-02, - 334 B/Shanghai-Songjiang/1204/2011_2011-05-04, - 335 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-End; diff --git a/tests/data/MERS_274_sCoal.combinedTyped.mcc.tree b/tests/data/MERS.mcc.tree similarity index 100% rename from tests/data/MERS_274_sCoal.combinedTyped.mcc.tree rename to tests/data/MERS.mcc.tree diff --git a/tests/data/miniFluB.mcc.tree b/tests/data/miniFluB.mcc.tree new file mode 100644 index 0000000..8c7fc38 --- /dev/null +++ b/tests/data/miniFluB.mcc.tree @@ -0,0 +1,60 @@ +#NEXUS +begin taxa; + dimensions ntax=50; + taxlabels + 'B/Anhui-Huashan/1216/2011_2011-05-10' + 'B/Bangladesh/1994/2010_2010-01-20' + 'B/Bangladesh/3333/2007_2007' + 'B/Bangladesh/9673/2009_2009-11-01' + 'B/Beijing-Huairou/1338/2011_2011-03-10' + 'B/Beijing-Xicheng/1267/2011_2011-02-27' + 'B/Beijing-Xicheng/1291/2011_2011-03-09' + 'B/Beijing-Xicheng/1677/2011_2011-04-06' + 'B/Beijing-Xicheng/1962/2011_2011-05-23' + 'B/Chongqing-Wanzhou/1152/2011_2011-03-08' + 'B/Chongqing-Wanzhou/145/2011_2011-02-03' + 'B/Fujian-Cangshan/1194/2010_2010-05-10' + 'B/Fujian-Gulou/1553/2011_2011-08-31' + 'B/Fujian-Meilie/1440/2010_2010-08-19' + 'B/Gansu-Chengguan/572/2011_2011-03-10' + 'B/Guangdong-Chikan/1370/2010_2010-07-26' + 'B/Guangdong-Dongguanbendi/1721/2010_2010-09-01' + 'B/Guangdong-Luohu/1512/2010_2010-06-21' + 'B/HONG_KONG/2196/2010_2010-11-30' + 'B/Heilongjiang-Gongnong/182/2011_2011-02-16' + 'B/Hubei-Wuchang/1108/2011_2011-04-03' + 'B/Hubei-Wujiagang/1112/2010_2010-08-27' + 'B/Hubei-Wujiagang/158/2009_2009' + 'B/Hunan-Beihu/1300/2011_2011-05-26' + 'B/Hunan-Lusong/1126/2011_2011-02-16' + 'B/Hunan-Yuhu/134/2011_2011-03-02' + 'B/Hunan-Yuhua/11100/2010_2010-09-08' + 'B/Jiangsu-Beitang/1135/2011_2011-04-05' + 'B/Jiangsu-Quanshan/1329/2011_2011-04-27' + 'B/Jiangsu-Xinpu/192/2011_2011-03-02' + 'B/Shaanxi-Beilin/1165/2011_2011-02-15' + 'B/Shanghai-Baoshan/197/2011_2011-03-07' + 'B/Shanghai-Luwan/1188/2011_2011-04-12' + 'B/Shanghai-Luwan/1217/2011_2011-05-04' + 'B/Shanghai-Luwan/187/2011_2011-02-15' + 'B/Shanghai-Pudongxin/1238/2011_2011-05-13' + 'B/Shanghai-Pudongxin/1467/2010_2010-05-05' + 'B/Shanghai-Songjiang/1108/2011_2011-03-02' + 'B/Shanghai-Zhangning/1133/2011_2011-02-24' + 'B/Shanghai-Zhangning/1143/2011_2011-03-01' + 'B/Shanghai-Zhangning/1423/2010_2010-06-11' + 'B/Sichuan-Anyue/139/2011_2011-03-02' + 'B/Sichuan-Qingyang/1305/2010_2010-07-11' + 'B/Sichuan-Yucheng/1212/2011_2011-04-03' + 'B/Texas/06/2011_2011-02-16' + 'B/Tianjin-Binhaixin/1125/2011_2011-04-12' + 'B/Tianjin-Hedong/1174/2011_2011-05-15' + 'B/Tianjin-Hexi/1112/2011_2011-03-18' + 'B/Tianjin-Hexi/156/2011_2011-02-15' + 'B/Tianjin-Hexi/180/2011_2011-02-28' +; +end; + +begin trees; + tree tree_1 = [&R] 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+end; diff --git a/tests/testsuite.py b/tests/testsuite.py index f14e05d..7036fcb 100644 --- a/tests/testsuite.py +++ b/tests/testsuite.py @@ -6,11 +6,11 @@ class test_parsers(unittest.TestCase): def test_beast1_traits(self): print('Testing BEAST v1 trait parsing') - ll=bt.loadNexus('./data/InfB_HAt_ALLs1.mcc.tree',tip_regex='_([0-9-]+)') + ll=bt.loadNexus('./data/miniFluB.mcc.tree',tip_regex='_([0-9-]+)') ll.traverse_tree() print('Test if branches have correct number of traits') - assert len(ll.root.traits)==34 + assert len(ll.root.traits)==77 print('Root has correct number of traits') for k in ll.Objects: @@ -23,7 +23,7 @@ def test_beast1_traits(self): def test_beast2_traits(self): print('Testing BEAST v2 trait parsing') - ll=bt.loadNexus('./data/MERS_274_sCoal.combinedTyped.mcc.tree') + ll=bt.loadNexus('./data/MERS.mcc.tree') ll.traverse_tree() print('Test if branches have correct number of traits')