Example trait file for examples/nexus/Flu.nex included with BEAST 2.

times.txt

traits  time
TREESPARROW_HENAN_1_2004        1
HUMAN_VIETNAM_CL105_2005        2
TREESPARROW_HENAN_4_2004        3
CHICKEN_HEBEI_326_2005  4
CHICKEN_HONGKONG_915_1997       5
VIETNAM_3062_2004       6
GOOSE_HONGKONG_W355_1997        7
DUCK_HONGKONG_Y283_1997 8
DUCK_VIETNAM_376_2005   9
MALLARD_VIETNAM_16_2003 10
CHICKEN_THAILAND_KANCHANABURI_CK_160_2005       11
DUCK_GUANGZHOU_20_2005  12
CK_HK_WF157_2003        13
SWINE_ANHUI_2004        14
DUCK_VIETNAM_272_2005   15
HONGKONG_1997_1998      16
GOOSE_SHANTOU_2216_2005 17
TREESPARROW_HENAN_3_2004        18
PEREGRINEFALCON_HK_D0028_2004   19
TREESPARROW_HENAN_2_2004        20
HONGKONG_538_1997       2

The times don't seem to represent the dates? Shouldn't it look something like:

traits time
TREESPARROW_HENAN_1_2004 2004
HUMAN_VIETNAM_CL105_2005 2005
TREESPARROW_HENAN_4_2004 2004
CHICKEN_HEBEI_326_2005 2005
CHICKEN_HONGKONG_915_1997 1997
VIETNAM_3062_2004 2004
GOOSE_HONGKONG_W355_1997 1997
DUCK_HONGKONG_Y283_1997 1997
DUCK_VIETNAM_376_2005 2005
MALLARD_VIETNAM_16_2003 2003
CHICKEN_THAILAND_KANCHANABURI_CK_160_2005 2005
DUCK_GUANGZHOU_20_2005 2005
CK_HK_WF157_2003 2003
SWINE_ANHUI_2004 2004
DUCK_VIETNAM_272_2005 2005
HONGKONG_1997_1998 1998
GOOSE_SHANTOU_2216_2005 2005
TREESPARROW_HENAN_3_2004 2004
PEREGRINEFALCON_HK_D0028_2004 2004
TREESPARROW_HENAN_2_2004 2004
HONGKONG_538_1997 1997

I wasn't able to use the guess dates, from file option using either of these trait files and the flu.nex example.

Hi Alexei, I was just trying to illustrate a way of getting non-zero tip heights from a file - not any particular dates. (Scarpino's not interested in the Flu data anyway.) Scarpino, unfortunately pasting into gist has stripped out the tabs somehow, so this doesn't work. If you have a text file with tabs separating the two columns and a header up the top, it should work though. (Indeed this one did work, prior to it being mangled by my web browser!)