1 <?xml version="1.0" standalone="yes"?>
\r
3 <!-- Generated by BEAUTi v1.7.4 -->
\r
4 <!-- by Alexei J. Drummond, Andrew Rambaut and Marc A. Suchard -->
\r
5 <!-- Department of Computer Science, University of Auckland and -->
\r
6 <!-- Institute of Evolutionary Biology, University of Edinburgh -->
\r
7 <!-- David Geffen School of Medicine, University of California, Los Angeles-->
\r
8 <!-- http://beast.bio.ed.ac.uk/ -->
\r
11 <!-- The list of taxa to be analysed (can also include dates/ages). -->
\r
14 <taxon id="179_Avian_H1N6_USA_1976">
\r
15 <date value="1976.0" direction="forwards" units="years"/>
\r
17 <taxon id="165_Avian_H1N1_Canada_1977">
\r
18 <date value="1977.0" direction="forwards" units="years"/>
\r
20 <taxon id="177_Avian_H1N1_Canada_1977">
\r
21 <date value="1977.0" direction="forwards" units="years"/>
\r
23 <taxon id="105_Avian_H1N1_Canada_1976">
\r
24 <date value="1976.0" direction="forwards" units="years"/>
\r
26 <taxon id="267_Avian_H1N1_Canada_1976">
\r
27 <date value="1976.0" direction="forwards" units="years"/>
\r
29 <taxon id="195_Avian_H1N6_Canada_1977">
\r
30 <date value="1977.0" direction="forwards" units="years"/>
\r
32 <taxon id="162_Avian_H1N1_Canada_1977">
\r
33 <date value="1977.0" direction="forwards" units="years"/>
\r
35 <taxon id="213_Avian_H1N5_USA_1978">
\r
36 <date value="1978.0" direction="forwards" units="years"/>
\r
38 <taxon id="164_Avian_H1N1_Canada_1979">
\r
39 <date value="1979.0" direction="forwards" units="years"/>
\r
41 <taxon id="163_Avian_H1N1_Canada_1979">
\r
42 <date value="1979.0" direction="forwards" units="years"/>
\r
44 <taxon id="158_Avian_H1N1_USA_1981">
\r
45 <date value="1981.0" direction="forwards" units="years"/>
\r
47 <taxon id="309_Avian_H1N1_USA_1980">
\r
48 <date value="1980.0" direction="forwards" units="years"/>
\r
50 <taxon id="153_Avian_H1N5_Canada_1981">
\r
51 <date value="1981.0" direction="forwards" units="years"/>
\r
53 <taxon id="156_Avian_H1N1_Canada_2002">
\r
54 <date value="2002.0" direction="forwards" units="years"/>
\r
56 <taxon id="196_Avian_H1N1_Canada_1998">
\r
57 <date value="1998.0" direction="forwards" units="years"/>
\r
59 <taxon id="180_Avian_H1N9_USA_1987">
\r
60 <date value="1987.0" direction="forwards" units="years"/>
\r
62 <taxon id="274_Avian_H1N1_USA_1987">
\r
63 <date value="1987.0" direction="forwards" units="years"/>
\r
65 <taxon id="279_Avian_H1N1_USA_1980">
\r
66 <date value="1980.0" direction="forwards" units="years"/>
\r
68 <taxon id="116_Avian_H1N1_USA_1985">
\r
69 <date value="1985.0" direction="forwards" units="years"/>
\r
71 <taxon id="106_Avian_H1N1_USA_1981">
\r
72 <date value="1981.0" direction="forwards" units="years"/>
\r
74 <taxon id="199_Avian_H1N2_USA_1982">
\r
75 <date value="1982.0" direction="forwards" units="years"/>
\r
77 <taxon id="155_Avian_H1N1_Canada_1988">
\r
78 <date value="1988.0" direction="forwards" units="years"/>
\r
80 <taxon id="169_Avian_H1N1_USA_1987">
\r
81 <date value="1987.0" direction="forwards" units="years"/>
\r
83 <taxon id="264_Avian_H1N1_USA_1986">
\r
84 <date value="1986.0" direction="forwards" units="years"/>
\r
86 <taxon id="197_Avian_H1N1_USA_1990">
\r
87 <date value="1990.0" direction="forwards" units="years"/>
\r
89 <taxon id="289_Avian_H1N1_USA_1993">
\r
90 <date value="1993.0" direction="forwards" units="years"/>
\r
92 <taxon id="255_Avian_H1N1_USA_1994">
\r
93 <date value="1994.0" direction="forwards" units="years"/>
\r
95 <taxon id="181_Avian_H1N1_USA_1993">
\r
96 <date value="1993.0" direction="forwards" units="years"/>
\r
98 <taxon id="200_Avian_H1N1_USA_1993">
\r
99 <date value="1993.0" direction="forwards" units="years"/>
\r
101 <taxon id="154_Avian_H1N1_Canada_1996">
\r
102 <date value="1996.0" direction="forwards" units="years"/>
\r
104 <taxon id="198_Avian_H1N1_USA_1999">
\r
105 <date value="1999.0" direction="forwards" units="years"/>
\r
107 <taxon id="223_Avian_H1N1_USA_2002">
\r
108 <date value="2002.0" direction="forwards" units="years"/>
\r
110 <taxon id="224_Avian_H1N1_USA_2007">
\r
111 <date value="2007.0" direction="forwards" units="years"/>
\r
113 <taxon id="233_Avian_H1N1_USA_2005">
\r
114 <date value="2005.0" direction="forwards" units="years"/>
\r
116 <taxon id="182_Avian_H1N6_USA_2002">
\r
117 <date value="2002.0" direction="forwards" units="years"/>
\r
119 <taxon id="302_Avian_H1N1_USA_2003">
\r
120 <date value="2003.0" direction="forwards" units="years"/>
\r
122 <taxon id="303_Avian_H1N1_USA_2003">
\r
123 <date value="2003.0" direction="forwards" units="years"/>
\r
125 <taxon id="157_Avian_H1N3_NewZealand_1976">
\r
126 <date value="1976.0" direction="forwards" units="years"/>
\r
128 <taxon id="125_Avian_H1N1_Japan_1977">
\r
129 <date value="1977.0" direction="forwards" units="years"/>
\r
131 <taxon id="285_Avian_H1N1_HongKong_1979">
\r
132 <date value="1979.0" direction="forwards" units="years"/>
\r
134 <taxon id="132_Avian_H1N1_Australia_1980">
\r
135 <date value="1980.0" direction="forwards" units="years"/>
\r
137 <taxon id="102_Avian_H1N1_Japan_1996">
\r
138 <date value="1996.0" direction="forwards" units="years"/>
\r
140 <taxon id="126_Avian_H1N9_Japan_1998">
\r
141 <date value="1998.0" direction="forwards" units="years"/>
\r
143 <taxon id="307_Avian_H1N1_Italy_2003">
\r
144 <date value="2003.0" direction="forwards" units="years"/>
\r
146 <taxon id="276_Avian_H1N1_Italy_2007">
\r
147 <date value="2007.0" direction="forwards" units="years"/>
\r
149 <taxon id="277_Avian_H1N1_Italy_2006">
\r
150 <date value="2006.0" direction="forwards" units="years"/>
\r
152 <taxon id="133_Avian_H1N1_Germany_1977">
\r
153 <date value="1977.0" direction="forwards" units="years"/>
\r
155 <taxon id="248_Avian_H1_HongKong_1977">
\r
156 <date value="1977.0" direction="forwards" units="years"/>
\r
158 <taxon id="134_Swine_H1N1_Netherlands_1980">
\r
159 <date value="1980.0" direction="forwards" units="years"/>
\r
161 <taxon id="234_Swine_H1N1_Belgium_1979">
\r
162 <date value="1979.0" direction="forwards" units="years"/>
\r
164 <taxon id="237_Swine_H1N1_France_1984">
\r
165 <date value="1984.0" direction="forwards" units="years"/>
\r
167 <taxon id="107_Swine_H1N1_Netherlands_1985">
\r
168 <date value="1985.0" direction="forwards" units="years"/>
\r
170 <taxon id="117_Swine_H1N1_Belgium_1983">
\r
171 <date value="1983.0" direction="forwards" units="years"/>
\r
173 <taxon id="135_Swine_H1N1_Italy_1987">
\r
174 <date value="1987.0" direction="forwards" units="years"/>
\r
176 <taxon id="149_Swine_H1N1_Germany_1995">
\r
177 <date value="1995.0" direction="forwards" units="years"/>
\r
179 <taxon id="235_Swine_H1N1_France_1995">
\r
180 <date value="1995.0" direction="forwards" units="years"/>
\r
182 <taxon id="288_Swine_H1N1_Germany_1992">
\r
183 <date value="1992.0" direction="forwards" units="years"/>
\r
185 <taxon id="227_Swine_H1N1_Spain_1991">
\r
186 <date value="1991.0" direction="forwards" units="years"/>
\r
188 <taxon id="226_Swine_H1N1_France_1985">
\r
189 <date value="1985.0" direction="forwards" units="years"/>
\r
191 <taxon id="238_Swine_H1N1_UnitedKingdom_1992">
\r
192 <date value="1992.0" direction="forwards" units="years"/>
\r
194 <taxon id="210_Swine_H1N1_UnitedKingdom_1995">
\r
195 <date value="1995.0" direction="forwards" units="years"/>
\r
197 <taxon id="236_Swine_H1N1_UnitedKingdom_1996">
\r
198 <date value="1996.0" direction="forwards" units="years"/>
\r
200 <taxon id="225_Swine_H1N1_UnitedKingdom_1993">
\r
201 <date value="1993.0" direction="forwards" units="years"/>
\r
203 <taxon id="212_Swine_H1N1_UnitedKingdom_1999">
\r
204 <date value="1999.0" direction="forwards" units="years"/>
\r
206 <taxon id="246_Swine_H1N1_UnitedKingdom_1994">
\r
207 <date value="1994.0" direction="forwards" units="years"/>
\r
209 <taxon id="211_Swine_H1N1_UnitedKingdom_1998">
\r
210 <date value="1998.0" direction="forwards" units="years"/>
\r
212 <taxon id="247_Swine_H1N1_UnitedKingdom_1997">
\r
213 <date value="1997.0" direction="forwards" units="years"/>
\r
215 <taxon id="141_Swine_H1N1_Italy_1997">
\r
216 <date value="1997.0" direction="forwards" units="years"/>
\r
218 <taxon id="123_Swine_H1N1_Italy_1996">
\r
219 <date value="1996.0" direction="forwards" units="years"/>
\r
221 <taxon id="140_Swine_H1N1_Italy_1998">
\r
222 <date value="1998.0" direction="forwards" units="years"/>
\r
224 <taxon id="191_Swine_H1N1_Italy_1997">
\r
225 <date value="1997.0" direction="forwards" units="years"/>
\r
227 <taxon id="310_Swine_H1N1_Germany_1993">
\r
228 <date value="1993.0" direction="forwards" units="years"/>
\r
230 <taxon id="228_Swine_H1N1_Denmark_1993">
\r
231 <date value="1993.0" direction="forwards" units="years"/>
\r
233 <taxon id="305_Swine_H1N1_Belgium_1998">
\r
234 <date value="1998.0" direction="forwards" units="years"/>
\r
236 <taxon id="168_Swine_H1N1_Spain_2003">
\r
237 <date value="2003.0" direction="forwards" units="years"/>
\r
239 <taxon id="159_Swine_H1N1_Spain_2004">
\r
240 <date value="2004.0" direction="forwards" units="years"/>
\r
242 <taxon id="278_Swine_H1N1_Hungary_2006">
\r
243 <date value="2006.0" direction="forwards" units="years"/>
\r
245 <taxon id="124_Swine_H1N1_France_1999">
\r
246 <date value="1999.0" direction="forwards" units="years"/>
\r
248 <taxon id="304_Swine_H1N1_China_2007">
\r
249 <date value="2007.0" direction="forwards" units="years"/>
\r
251 <taxon id="287_Swine_H1N1_Germany_2003">
\r
252 <date value="2003.0" direction="forwards" units="years"/>
\r
254 <taxon id="167_Swine_H1N1_Spain_2003">
\r
255 <date value="2003.0" direction="forwards" units="years"/>
\r
257 <taxon id="192_Swine_H1N2_Germany_2000">
\r
258 <date value="2000.0" direction="forwards" units="years"/>
\r
260 <taxon id="1_Human_H1N1_USA_1918">
\r
261 <date value="1918.0" direction="forwards" units="years"/>
\r
263 <taxon id="3_Human_H1N1_UnitedKingdom_1933">
\r
264 <date value="1933.0" direction="forwards" units="years"/>
\r
266 <taxon id="2_Human_H1N1_UnitedKingdom_1933">
\r
267 <date value="1933.0" direction="forwards" units="years"/>
\r
269 <taxon id="23_Human_H1_Japan_1967">
\r
270 <date value="1967.0" direction="forwards" units="years"/>
\r
272 <taxon id="7_Human_H1N1_Australia_1935">
\r
273 <date value="1935.0" direction="forwards" units="years"/>
\r
275 <taxon id="6_Human_H1N1_USA_1935">
\r
276 <date value="1935.0" direction="forwards" units="years"/>
\r
278 <taxon id="8_Human_H1N1_1936">
\r
279 <date value="1936.0" direction="forwards" units="years"/>
\r
281 <taxon id="4_Human_H1N1_PuertoRico_1934">
\r
282 <date value="1934.0" direction="forwards" units="years"/>
\r
284 <taxon id="5_Human_H1N1_PuertoRico_1934">
\r
285 <date value="1934.0" direction="forwards" units="years"/>
\r
287 <taxon id="10_Human_H1N1_USA_1942">
\r
288 <date value="1942.0" direction="forwards" units="years"/>
\r
290 <taxon id="11_Human_H1N1_USA_1943">
\r
291 <date value="1943.0" direction="forwards" units="years"/>
\r
293 <taxon id="12_Human_H1N1_USA_1943">
\r
294 <date value="1943.0" direction="forwards" units="years"/>
\r
296 <taxon id="13_Human_H1N1_USA_1945">
\r
297 <date value="1945.0" direction="forwards" units="years"/>
\r
299 <taxon id="9_Human_H1N1_USA_1940">
\r
300 <date value="1940.0" direction="forwards" units="years"/>
\r
302 <taxon id="14_Human_H1N1_1946">
\r
303 <date value="1946.0" direction="forwards" units="years"/>
\r
305 <taxon id="15_Human_H1N1_USA_1947">
\r
306 <date value="1947.0" direction="forwards" units="years"/>
\r
308 <taxon id="16_Human_H1N1_USA_1947">
\r
309 <date value="1947.0" direction="forwards" units="years"/>
\r
311 <taxon id="18_Human_H1N1_USA_1950">
\r
312 <date value="1950.0" direction="forwards" units="years"/>
\r
314 <taxon id="22_Human_H1N1_USA_1957">
\r
315 <date value="1957.0" direction="forwards" units="years"/>
\r
317 <taxon id="19_Human_H1N1_USA_1951">
\r
318 <date value="1951.0" direction="forwards" units="years"/>
\r
320 <taxon id="20_Human_H1N1_Malaysia_1954">
\r
321 <date value="1954.0" direction="forwards" units="years"/>
\r
323 <taxon id="17_Human_H1N1_USA_1948">
\r
324 <date value="1948.0" direction="forwards" units="years"/>
\r
326 <taxon id="21_Human_H1N1_Russia_1954">
\r
327 <date value="1954.0" direction="forwards" units="years"/>
\r
329 <taxon id="26_Human_H1N1_HongKong_1977_1954">
\r
330 <date value="1954.0" direction="forwards" units="years"/>
\r
332 <taxon id="27_Human_H1N1_USA_1978_1955">
\r
333 <date value="1955.0" direction="forwards" units="years"/>
\r
335 <taxon id="31_Human_H1N1_USA_1983_1960">
\r
336 <date value="1960.0" direction="forwards" units="years"/>
\r
338 <taxon id="29_Human_H1N1_UnitedKingdom_1982_1959">
\r
339 <date value="1959.0" direction="forwards" units="years"/>
\r
341 <taxon id="30_Human_H1N1_Fiji_1983_1960">
\r
342 <date value="1960.0" direction="forwards" units="years"/>
\r
344 <taxon id="28_Human_H1N1_India_1980_1957">
\r
345 <date value="1957.0" direction="forwards" units="years"/>
\r
347 <taxon id="33_Human_H1N1_USA_1986_1963">
\r
348 <date value="1963.0" direction="forwards" units="years"/>
\r
350 <taxon id="36_Human_H1N1_Italy_1989_1966">
\r
351 <date value="1966.0" direction="forwards" units="years"/>
\r
353 <taxon id="39_Human_H1N1_Mongolia_1991_1968">
\r
354 <date value="1968.0" direction="forwards" units="years"/>
\r
356 <taxon id="35_Human_H1N1_Japan_1989_1966">
\r
357 <date value="1966.0" direction="forwards" units="years"/>
\r
359 <taxon id="37_Human_H1N1_Italy_1989_1966">
\r
360 <date value="1966.0" direction="forwards" units="years"/>
\r
362 <taxon id="38_Human_H1N1_USA_1991_1968">
\r
363 <date value="1968.0" direction="forwards" units="years"/>
\r
365 <taxon id="44_Human_H1N1_USA_1995_1972">
\r
366 <date value="1972.0" direction="forwards" units="years"/>
\r
368 <taxon id="43_Human_H1N1_Switzerland_1995_1972">
\r
369 <date value="1972.0" direction="forwards" units="years"/>
\r
371 <taxon id="55_Human_H1N1_Australia_2000_1977">
\r
372 <date value="1977.0" direction="forwards" units="years"/>
\r
374 <taxon id="41_Human_H1N1_USA_1995_1972">
\r
375 <date value="1972.0" direction="forwards" units="years"/>
\r
377 <taxon id="48_Human_H1N1_Taiwan_1996_1973">
\r
378 <date value="1973.0" direction="forwards" units="years"/>
\r
380 <taxon id="42_Human_H1N1_China_1995_1972">
\r
381 <date value="1972.0" direction="forwards" units="years"/>
\r
383 <taxon id="45_Human_H1N1_USA_1995_1972">
\r
384 <date value="1972.0" direction="forwards" units="years"/>
\r
386 <taxon id="47_Human_H1N1_USA_1996_1973">
\r
387 <date value="1973.0" direction="forwards" units="years"/>
\r
389 <taxon id="40_Human_H1N1_China_1995_1972">
\r
390 <date value="1972.0" direction="forwards" units="years"/>
\r
392 <taxon id="46_Human_H1N1_China_1996_1973">
\r
393 <date value="1973.0" direction="forwards" units="years"/>
\r
395 <taxon id="52_Human_H1N1_HongKong_1998_1975">
\r
396 <date value="1975.0" direction="forwards" units="years"/>
\r
398 <taxon id="49_Human_H1N1_Taiwan_1997_1974">
\r
399 <date value="1974.0" direction="forwards" units="years"/>
\r
401 <taxon id="51_Human_H1N1_HongKong_1998_1975">
\r
402 <date value="1975.0" direction="forwards" units="years"/>
\r
404 <taxon id="50_Human_H1N1_HongKong_1998_1975">
\r
405 <date value="1975.0" direction="forwards" units="years"/>
\r
407 <taxon id="60_Human_H1N1_Taiwan_2002_1979">
\r
408 <date value="1979.0" direction="forwards" units="years"/>
\r
410 <taxon id="54_Human_H1N1_NewCaledonia_1999_1976">
\r
411 <date value="1976.0" direction="forwards" units="years"/>
\r
413 <taxon id="53_Human_H1N1_Taiwan_1999_1976">
\r
414 <date value="1976.0" direction="forwards" units="years"/>
\r
416 <taxon id="56_Human_H1N1_USA_2000_1977">
\r
417 <date value="1977.0" direction="forwards" units="years"/>
\r
419 <taxon id="57_Human_H1N1_NewZealand_2000_1977">
\r
420 <date value="1977.0" direction="forwards" units="years"/>
\r
422 <taxon id="58_Human_H1N1_NewZealand_2000_1977">
\r
423 <date value="1977.0" direction="forwards" units="years"/>
\r
425 <taxon id="61_Human_H1N2_USA_2002_1979">
\r
426 <date value="1979.0" direction="forwards" units="years"/>
\r
428 <taxon id="62_Human_H1N2_Denmark_2003_1980">
\r
429 <date value="1980.0" direction="forwards" units="years"/>
\r
431 <taxon id="64_Human_H1N2_USA_2003_1980">
\r
432 <date value="1980.0" direction="forwards" units="years"/>
\r
434 <taxon id="59_Human_H1N1_Japan_2001_1978">
\r
435 <date value="1978.0" direction="forwards" units="years"/>
\r
437 <taxon id="63_Human_H1N1_USA_2003_1980">
\r
438 <date value="1980.0" direction="forwards" units="years"/>
\r
440 <taxon id="65_Human_H1N1_Denmark_2004_1981">
\r
441 <date value="1981.0" direction="forwards" units="years"/>
\r
443 <taxon id="68_Human_H1N1_Australia_2005_1982">
\r
444 <date value="1982.0" direction="forwards" units="years"/>
\r
446 <taxon id="79_Human_H1N1_USA_2007_1984">
\r
447 <date value="1984.0" direction="forwards" units="years"/>
\r
449 <taxon id="76_Human_H1N1_USA_2006_1983">
\r
450 <date value="1983.0" direction="forwards" units="years"/>
\r
452 <taxon id="82_Human_H1N1_USA_2007_1984">
\r
453 <date value="1984.0" direction="forwards" units="years"/>
\r
455 <taxon id="72_Human_H1N1_Thailand_2006_1983">
\r
456 <date value="1983.0" direction="forwards" units="years"/>
\r
458 <taxon id="77_Human_H1N1_SolomonIslands_2006_1983">
\r
459 <date value="1983.0" direction="forwards" units="years"/>
\r
461 <taxon id="74_Human_H1N1_China_2006_1983">
\r
462 <date value="1983.0" direction="forwards" units="years"/>
\r
464 <taxon id="75_Human_H1N1_China_2006_1983">
\r
465 <date value="1983.0" direction="forwards" units="years"/>
\r
467 <taxon id="81_Human_H1N1_USA_2007_1984">
\r
468 <date value="1984.0" direction="forwards" units="years"/>
\r
470 <taxon id="71_Human_H1N1_China_2006_1983">
\r
471 <date value="1983.0" direction="forwards" units="years"/>
\r
473 <taxon id="73_Human_H1N1_China_2006_1983">
\r
474 <date value="1983.0" direction="forwards" units="years"/>
\r
476 <taxon id="98_Human_H1N1_USA_2008_1985">
\r
477 <date value="1985.0" direction="forwards" units="years"/>
\r
479 <taxon id="83_Human_H1N1_USA_2007_1984">
\r
480 <date value="1984.0" direction="forwards" units="years"/>
\r
482 <taxon id="84_Human_H1N1_USA_2007_1984">
\r
483 <date value="1984.0" direction="forwards" units="years"/>
\r
485 <taxon id="67_Human_H1N1_NewZealand_2004_1981">
\r
486 <date value="1981.0" direction="forwards" units="years"/>
\r
488 <taxon id="97_Human_H1N1_Australia_2008_1985">
\r
489 <date value="1985.0" direction="forwards" units="years"/>
\r
491 <taxon id="78_Human_H1N1_USA_2006_1983">
\r
492 <date value="1983.0" direction="forwards" units="years"/>
\r
494 <taxon id="80_Human_H1N1_USA_2007_1984">
\r
495 <date value="1984.0" direction="forwards" units="years"/>
\r
497 <taxon id="86_Human_H1N1_USA_2007_1984">
\r
498 <date value="1984.0" direction="forwards" units="years"/>
\r
500 <taxon id="92_Human_H1N1_USA_2008_1985">
\r
501 <date value="1985.0" direction="forwards" units="years"/>
\r
503 <taxon id="87_Human_H1N1_USA_2007_1984">
\r
504 <date value="1984.0" direction="forwards" units="years"/>
\r
506 <taxon id="88_Human_H1N1_USA_2007_1984">
\r
507 <date value="1984.0" direction="forwards" units="years"/>
\r
509 <taxon id="85_Human_H1N1_USA_2007_1984">
\r
510 <date value="1984.0" direction="forwards" units="years"/>
\r
512 <taxon id="95_Human_H1N1_USA_2008_1985">
\r
513 <date value="1985.0" direction="forwards" units="years"/>
\r
515 <taxon id="89_Human_H1N1_USA_2007_1984">
\r
516 <date value="1984.0" direction="forwards" units="years"/>
\r
518 <taxon id="93_Human_H1N1_USA_2008_1985">
\r
519 <date value="1985.0" direction="forwards" units="years"/>
\r
521 <taxon id="94_Human_H1N1_USA_2008_1985">
\r
522 <date value="1985.0" direction="forwards" units="years"/>
\r
524 <taxon id="96_Human_H1N1_USA_2008_1985">
\r
525 <date value="1985.0" direction="forwards" units="years"/>
\r
527 <taxon id="90_Human_H1N1_USA_2008_1985">
\r
528 <date value="1985.0" direction="forwards" units="years"/>
\r
530 <taxon id="100_Human_H1N1_USA_2008_1985">
\r
531 <date value="1985.0" direction="forwards" units="years"/>
\r
533 <taxon id="91_Human_H1N1_USA_2008_1985">
\r
534 <date value="1985.0" direction="forwards" units="years"/>
\r
536 <taxon id="99_Human_H1N1_USA_2008_1985">
\r
537 <date value="1985.0" direction="forwards" units="years"/>
\r
539 <taxon id="115_Swine_H1N1_USA_1930">
\r
540 <date value="1930.0" direction="forwards" units="years"/>
\r
542 <taxon id="166_Swine_H1N1_1931">
\r
543 <date value="1931.0" direction="forwards" units="years"/>
\r
545 <taxon id="292_Swine_H1N1_USA_1945">
\r
546 <date value="1945.0" direction="forwards" units="years"/>
\r
548 <taxon id="243_Swine_H1N1_USA_1942">
\r
549 <date value="1942.0" direction="forwards" units="years"/>
\r
551 <taxon id="244_Swine_H1N1_USA_1935">
\r
552 <date value="1935.0" direction="forwards" units="years"/>
\r
554 <taxon id="232_Swine_H1N1_USA_1957">
\r
555 <date value="1957.0" direction="forwards" units="years"/>
\r
557 <taxon id="104_Swine_H1N1_USA_1961">
\r
558 <date value="1961.0" direction="forwards" units="years"/>
\r
560 <taxon id="293_Swine_H1N1_USA_1968">
\r
561 <date value="1968.0" direction="forwards" units="years"/>
\r
563 <taxon id="219_Swine_H1N1_USA_1966">
\r
564 <date value="1966.0" direction="forwards" units="years"/>
\r
566 <taxon id="207_Swine_H1N1_USA_1967">
\r
567 <date value="1967.0" direction="forwards" units="years"/>
\r
569 <taxon id="190_Swine_H1N1_USA_1970">
\r
570 <date value="1970.0" direction="forwards" units="years"/>
\r
572 <taxon id="188_Swine_H1N1_USA_1971">
\r
573 <date value="1971.0" direction="forwards" units="years"/>
\r
575 <taxon id="257_Swine_H1N1_USA_1973">
\r
576 <date value="1973.0" direction="forwards" units="years"/>
\r
578 <taxon id="202_Swine_H1N1_USA_1975">
\r
579 <date value="1975.0" direction="forwards" units="years"/>
\r
581 <taxon id="308_Swine_H1N1_USA_1976">
\r
582 <date value="1976.0" direction="forwards" units="years"/>
\r
584 <taxon id="171_Swine_H1N1_USA_1977">
\r
585 <date value="1977.0" direction="forwards" units="years"/>
\r
587 <taxon id="240_Swine_H1N1_USA_1977">
\r
588 <date value="1977.0" direction="forwards" units="years"/>
\r
590 <taxon id="217_Swine_H1N1_USA_1977">
\r
591 <date value="1977.0" direction="forwards" units="years"/>
\r
593 <taxon id="242_Swine_H1N1_USA_1977">
\r
594 <date value="1977.0" direction="forwards" units="years"/>
\r
596 <taxon id="214_Swine_H1N1_USA_1976">
\r
597 <date value="1976.0" direction="forwards" units="years"/>
\r
599 <taxon id="170_Swine_H1N1_USA_1976">
\r
600 <date value="1976.0" direction="forwards" units="years"/>
\r
602 <taxon id="178_Swine_H1N1_USA_1977">
\r
603 <date value="1977.0" direction="forwards" units="years"/>
\r
605 <taxon id="205_Swine_H1N1_USA_1977">
\r
606 <date value="1977.0" direction="forwards" units="years"/>
\r
608 <taxon id="184_Swine_H1N1_USA_1977">
\r
609 <date value="1977.0" direction="forwards" units="years"/>
\r
611 <taxon id="187_Swine_H1N1_USA_1978">
\r
612 <date value="1978.0" direction="forwards" units="years"/>
\r
614 <taxon id="144_Swine_H1N1_Japan_1977">
\r
615 <date value="1977.0" direction="forwards" units="years"/>
\r
617 <taxon id="290_Swine_H1N1_UnitedKingdom_1993">
\r
618 <date value="1993.0" direction="forwards" units="years"/>
\r
620 <taxon id="312_Swine_H1N1_UnitedKingdom_1986">
\r
621 <date value="1986.0" direction="forwards" units="years"/>
\r
623 <taxon id="103_Swine_H1N1_Japan_1979">
\r
624 <date value="1979.0" direction="forwards" units="years"/>
\r
626 <taxon id="113_Swine_H1N2_Japan_1996">
\r
627 <date value="1996.0" direction="forwards" units="years"/>
\r
629 <taxon id="110_Swine_H1N2_Japan_2003">
\r
630 <date value="2003.0" direction="forwards" units="years"/>
\r
632 <taxon id="128_Swine_H1N2_Japan_2006">
\r
633 <date value="2006.0" direction="forwards" units="years"/>
\r
635 <taxon id="183_Swine_H1N1_USA_1976">
\r
636 <date value="1976.0" direction="forwards" units="years"/>
\r
638 <taxon id="209_Swine_H1N1_USA_1978">
\r
639 <date value="1978.0" direction="forwards" units="years"/>
\r
641 <taxon id="231_Swine_H1N1_USA_1977">
\r
642 <date value="1977.0" direction="forwards" units="years"/>
\r
644 <taxon id="127_Swine_H1N2_Japan_1980">
\r
645 <date value="1980.0" direction="forwards" units="years"/>
\r
647 <taxon id="145_Swine_H1N1_Japan_1981">
\r
648 <date value="1981.0" direction="forwards" units="years"/>
\r
650 <taxon id="215_Swine_H1N1_USA_1976">
\r
651 <date value="1976.0" direction="forwards" units="years"/>
\r
653 <taxon id="218_Swine_H1N1_USA_1977">
\r
654 <date value="1977.0" direction="forwards" units="years"/>
\r
656 <taxon id="221_Swine_H1N1_USA_1978">
\r
657 <date value="1978.0" direction="forwards" units="years"/>
\r
659 <taxon id="208_Swine_H1N1_USA_1978">
\r
660 <date value="1978.0" direction="forwards" units="years"/>
\r
662 <taxon id="220_Swine_H1N1_USA_1978">
\r
663 <date value="1978.0" direction="forwards" units="years"/>
\r
665 <taxon id="112_Swine_H1N2_Thailand_2005">
\r
666 <date value="2005.0" direction="forwards" units="years"/>
\r
668 <taxon id="261_Swine_H1N1_Thailand_2005">
\r
669 <date value="2005.0" direction="forwards" units="years"/>
\r
671 <taxon id="143_Swine_H1N1_Thailand_2004">
\r
672 <date value="2004.0" direction="forwards" units="years"/>
\r
674 <taxon id="262_Swine_H1N1_Thailand_2005">
\r
675 <date value="2005.0" direction="forwards" units="years"/>
\r
677 <taxon id="206_Swine_H1N1_USA_1980">
\r
678 <date value="1980.0" direction="forwards" units="years"/>
\r
680 <taxon id="186_Swine_H1N1_USA_1979">
\r
681 <date value="1979.0" direction="forwards" units="years"/>
\r
683 <taxon id="189_Swine_H1N1_USA_1980">
\r
684 <date value="1980.0" direction="forwards" units="years"/>
\r
686 <taxon id="203_Swine_H1N1_Canada_1981">
\r
687 <date value="1981.0" direction="forwards" units="years"/>
\r
689 <taxon id="216_Swine_H1N1_Canada_1981">
\r
690 <date value="1981.0" direction="forwards" units="years"/>
\r
692 <taxon id="222_Swine_H1N1_USA_1987">
\r
693 <date value="1987.0" direction="forwards" units="years"/>
\r
695 <taxon id="299_Swine_H1N1_USA_1992">
\r
696 <date value="1992.0" direction="forwards" units="years"/>
\r
698 <taxon id="268_Swine_H1N1_Canada_2004">
\r
699 <date value="2004.0" direction="forwards" units="years"/>
\r
701 <taxon id="281_Swine_H1N1_Canada_2003">
\r
702 <date value="2003.0" direction="forwards" units="years"/>
\r
704 <taxon id="253_Swine_H1N1_Canada_2004">
\r
705 <date value="2004.0" direction="forwards" units="years"/>
\r
707 <taxon id="301_Swine_H1_Canada_1991">
\r
708 <date value="1991.0" direction="forwards" units="years"/>
\r
710 <taxon id="194_Swine_H1N2_Taiwan_2003">
\r
711 <date value="2003.0" direction="forwards" units="years"/>
\r
713 <taxon id="282_Swine_H1N2_Taiwan_2004">
\r
714 <date value="2004.0" direction="forwards" units="years"/>
\r
716 <taxon id="249_Swine_H1N1_Canada_2003">
\r
717 <date value="2003.0" direction="forwards" units="years"/>
\r
719 <taxon id="251_Swine_H1N1_Canada_2003">
\r
720 <date value="2003.0" direction="forwards" units="years"/>
\r
722 <taxon id="245_Swine_H1N1_USA_1986">
\r
723 <date value="1986.0" direction="forwards" units="years"/>
\r
725 <taxon id="185_Swine_H1N1_USA_1985">
\r
726 <date value="1985.0" direction="forwards" units="years"/>
\r
728 <taxon id="230_Swine_H1N1_USA_1987">
\r
729 <date value="1987.0" direction="forwards" units="years"/>
\r
731 <taxon id="142_Swine_H1N1_Thailand_2000">
\r
732 <date value="2000.0" direction="forwards" units="years"/>
\r
734 <taxon id="118_Swine_H1N1_USA_1997">
\r
735 <date value="1997.0" direction="forwards" units="years"/>
\r
737 <taxon id="175_Swine_H1N2_USA_2001">
\r
738 <date value="2001.0" direction="forwards" units="years"/>
\r
740 <taxon id="300_Swine_H1N1_USA_1988">
\r
741 <date value="1988.0" direction="forwards" units="years"/>
\r
743 <taxon id="111_Swine_H1N1_Thailand_2003">
\r
744 <date value="2003.0" direction="forwards" units="years"/>
\r
746 <taxon id="241_Swine_H1N1_USA_1988">
\r
747 <date value="1988.0" direction="forwards" units="years"/>
\r
749 <taxon id="201_Swine_H1N1_USA_1988">
\r
750 <date value="1988.0" direction="forwards" units="years"/>
\r
752 <taxon id="239_Swine_H1N1_China_2001">
\r
753 <date value="2001.0" direction="forwards" units="years"/>
\r
755 <taxon id="294_Swine_H1N1_China_2005">
\r
756 <date value="2005.0" direction="forwards" units="years"/>
\r
758 <taxon id="204_Swine_H1N1_USA_1991">
\r
759 <date value="1991.0" direction="forwards" units="years"/>
\r
761 <taxon id="136_Swine_H1N1_USA_1997">
\r
762 <date value="1997.0" direction="forwards" units="years"/>
\r
764 <taxon id="108_Swine_H1N1_USA_1997">
\r
765 <date value="1997.0" direction="forwards" units="years"/>
\r
767 <taxon id="109_Swine_H1N1_USA_1998">
\r
768 <date value="1998.0" direction="forwards" units="years"/>
\r
770 <taxon id="146_Swine_H1N1_USA_1998">
\r
771 <date value="1998.0" direction="forwards" units="years"/>
\r
773 <taxon id="280_Swine_H1N2_China_2004">
\r
774 <date value="2004.0" direction="forwards" units="years"/>
\r
776 <taxon id="284_Swine_H1N2_China_2005">
\r
777 <date value="2005.0" direction="forwards" units="years"/>
\r
779 <taxon id="306_Swine_H1N2_China_2007">
\r
780 <date value="2007.0" direction="forwards" units="years"/>
\r
782 <taxon id="271_Swine_H1N1_USA_1999">
\r
783 <date value="1999.0" direction="forwards" units="years"/>
\r
785 <taxon id="148_Swine_H1N2_USA_2000">
\r
786 <date value="2000.0" direction="forwards" units="years"/>
\r
788 <taxon id="138_Swine_H1N2_USA_2001">
\r
789 <date value="2001.0" direction="forwards" units="years"/>
\r
791 <taxon id="272_Swine_H1N1_USA_2002">
\r
792 <date value="2002.0" direction="forwards" units="years"/>
\r
794 <taxon id="172_Swine_H1N2_USA_2001">
\r
795 <date value="2001.0" direction="forwards" units="years"/>
\r
797 <taxon id="120_Swine_H1N2_USA_2001">
\r
798 <date value="2001.0" direction="forwards" units="years"/>
\r
800 <taxon id="193_Swine_H1N2_SouthKorea_2002">
\r
801 <date value="2002.0" direction="forwards" units="years"/>
\r
803 <taxon id="160_Swine_H1N2_USA_2001">
\r
804 <date value="2001.0" direction="forwards" units="years"/>
\r
806 <taxon id="260_Swine_H1N1_USA_2004">
\r
807 <date value="2004.0" direction="forwards" units="years"/>
\r
809 <taxon id="296_Swine_H1N1_SouthKorea_2004">
\r
810 <date value="2004.0" direction="forwards" units="years"/>
\r
812 <taxon id="297_Swine_H1N1_SouthKorea_2005">
\r
813 <date value="2005.0" direction="forwards" units="years"/>
\r
815 <taxon id="174_Swine_H1N2_USA_2001">
\r
816 <date value="2001.0" direction="forwards" units="years"/>
\r
818 <taxon id="147_Swine_H1N2_USA_2001">
\r
819 <date value="2001.0" direction="forwards" units="years"/>
\r
821 <taxon id="258_Swine_H1N2_USA_2001">
\r
822 <date value="2001.0" direction="forwards" units="years"/>
\r
824 <taxon id="139_Swine_H1N2_USA_2000">
\r
825 <date value="2000.0" direction="forwards" units="years"/>
\r
827 <taxon id="101_Human_H1N1_USA_2009">
\r
828 <date value="2009.0" direction="forwards" units="years"/>
\r
830 <taxon id="313_Human_H1N1_USA_2009">
\r
831 <date value="2009.0" direction="forwards" units="years"/>
\r
833 <taxon id="269_Swine_H1N2_China_2006">
\r
834 <date value="2006.0" direction="forwards" units="years"/>
\r
836 <taxon id="283_Swine_H1N2_China_2005">
\r
837 <date value="2005.0" direction="forwards" units="years"/>
\r
839 <taxon id="119_Swine_H1N2_USA_1999">
\r
840 <date value="1999.0" direction="forwards" units="years"/>
\r
842 <taxon id="173_Swine_H1N2_USA_2001">
\r
843 <date value="2001.0" direction="forwards" units="years"/>
\r
845 <taxon id="121_Swine_H1N2_USA_2001">
\r
846 <date value="2001.0" direction="forwards" units="years"/>
\r
848 <taxon id="122_Swine_H1N2_USA_2001">
\r
849 <date value="2001.0" direction="forwards" units="years"/>
\r
851 <taxon id="137_Swine_H1N2_USA_2001">
\r
852 <date value="2001.0" direction="forwards" units="years"/>
\r
854 <taxon id="263_Swine_H1N1_USA_2007">
\r
855 <date value="2007.0" direction="forwards" units="years"/>
\r
857 <taxon id="273_Swine_H1N2_USA_2003">
\r
858 <date value="2003.0" direction="forwards" units="years"/>
\r
860 <taxon id="151_Swine_H1N2_USA_2001">
\r
861 <date value="2001.0" direction="forwards" units="years"/>
\r
863 <taxon id="259_Swine_H1N2_USA_2004">
\r
864 <date value="2004.0" direction="forwards" units="years"/>
\r
866 <taxon id="291_Swine_H1N2_SouthKorea_2005">
\r
867 <date value="2005.0" direction="forwards" units="years"/>
\r
869 <taxon id="266_Swine_H1N2_SouthKorea_2005">
\r
870 <date value="2005.0" direction="forwards" units="years"/>
\r
872 <taxon id="298_Swine_H1N2_SouthKorea_2005">
\r
873 <date value="2005.0" direction="forwards" units="years"/>
\r
875 <taxon id="265_Swine_H1N2_SouthKorea_2004">
\r
876 <date value="2004.0" direction="forwards" units="years"/>
\r
878 <taxon id="275_Swine_H1N2_SouthKorea_2006">
\r
879 <date value="2006.0" direction="forwards" units="years"/>
\r
883 <!-- The sequence alignment (each sequence refers to a taxon above). -->
\r
884 <!-- ntax=289 nchar=1710 -->
\r
885 <alignment id="alignment" dataType="nucleotide">
\r
887 <taxon idref="179_Avian_H1N6_USA_1976"/>
\r
891 <taxon idref="165_Avian_H1N1_Canada_1977"/>
\r
895 <taxon idref="177_Avian_H1N1_Canada_1977"/>
\r
899 <taxon idref="105_Avian_H1N1_Canada_1976"/>
\r
903 <taxon idref="267_Avian_H1N1_Canada_1976"/>
\r
907 <taxon idref="195_Avian_H1N6_Canada_1977"/>
\r
911 <taxon idref="162_Avian_H1N1_Canada_1977"/>
\r
915 <taxon idref="213_Avian_H1N5_USA_1978"/>
\r
919 <taxon idref="164_Avian_H1N1_Canada_1979"/>
\r
923 <taxon idref="163_Avian_H1N1_Canada_1979"/>
\r
927 <taxon idref="158_Avian_H1N1_USA_1981"/>
\r
931 <taxon idref="309_Avian_H1N1_USA_1980"/>
\r
935 <taxon idref="153_Avian_H1N5_Canada_1981"/>
\r
939 <taxon idref="156_Avian_H1N1_Canada_2002"/>
\r
943 <taxon idref="196_Avian_H1N1_Canada_1998"/>
\r
947 <taxon idref="180_Avian_H1N9_USA_1987"/>
\r
951 <taxon idref="274_Avian_H1N1_USA_1987"/>
\r
955 <taxon idref="279_Avian_H1N1_USA_1980"/>
\r
959 <taxon idref="116_Avian_H1N1_USA_1985"/>
\r
963 <taxon idref="106_Avian_H1N1_USA_1981"/>
\r
967 <taxon idref="199_Avian_H1N2_USA_1982"/>
\r
971 <taxon idref="155_Avian_H1N1_Canada_1988"/>
\r
975 <taxon idref="169_Avian_H1N1_USA_1987"/>
\r
979 <taxon idref="264_Avian_H1N1_USA_1986"/>
\r
983 <taxon idref="197_Avian_H1N1_USA_1990"/>
\r
987 <taxon idref="289_Avian_H1N1_USA_1993"/>
\r
991 <taxon idref="255_Avian_H1N1_USA_1994"/>
\r
995 <taxon idref="181_Avian_H1N1_USA_1993"/>
\r
999 <taxon idref="200_Avian_H1N1_USA_1993"/>
\r
1003 <taxon idref="154_Avian_H1N1_Canada_1996"/>
\r
1007 <taxon idref="198_Avian_H1N1_USA_1999"/>
\r
1011 <taxon idref="223_Avian_H1N1_USA_2002"/>
\r
1015 <taxon idref="224_Avian_H1N1_USA_2007"/>
\r
1019 <taxon idref="233_Avian_H1N1_USA_2005"/>
\r
1023 <taxon idref="182_Avian_H1N6_USA_2002"/>
\r
1027 <taxon idref="302_Avian_H1N1_USA_2003"/>
\r
1031 <taxon idref="303_Avian_H1N1_USA_2003"/>
\r
1035 <taxon idref="157_Avian_H1N3_NewZealand_1976"/>
\r
1039 <taxon idref="125_Avian_H1N1_Japan_1977"/>
\r
1043 <taxon idref="285_Avian_H1N1_HongKong_1979"/>
\r
1047 <taxon idref="132_Avian_H1N1_Australia_1980"/>
\r
1051 <taxon idref="102_Avian_H1N1_Japan_1996"/>
\r
1055 <taxon idref="126_Avian_H1N9_Japan_1998"/>
\r
1059 <taxon idref="307_Avian_H1N1_Italy_2003"/>
\r
1063 <taxon idref="276_Avian_H1N1_Italy_2007"/>
\r
1067 <taxon idref="277_Avian_H1N1_Italy_2006"/>
\r
1071 <taxon idref="133_Avian_H1N1_Germany_1977"/>
\r
1075 <taxon idref="248_Avian_H1_HongKong_1977"/>
\r
1079 <taxon idref="134_Swine_H1N1_Netherlands_1980"/>
\r
1083 <taxon idref="234_Swine_H1N1_Belgium_1979"/>
\r
1087 <taxon idref="237_Swine_H1N1_France_1984"/>
\r
1091 <taxon idref="107_Swine_H1N1_Netherlands_1985"/>
\r
1095 <taxon idref="117_Swine_H1N1_Belgium_1983"/>
\r
1099 <taxon idref="135_Swine_H1N1_Italy_1987"/>
\r
1103 <taxon idref="149_Swine_H1N1_Germany_1995"/>
\r
1107 <taxon idref="235_Swine_H1N1_France_1995"/>
\r
1111 <taxon idref="288_Swine_H1N1_Germany_1992"/>
\r
1115 <taxon idref="227_Swine_H1N1_Spain_1991"/>
\r
1119 <taxon idref="226_Swine_H1N1_France_1985"/>
\r
1123 <taxon idref="238_Swine_H1N1_UnitedKingdom_1992"/>
\r
1127 <taxon idref="210_Swine_H1N1_UnitedKingdom_1995"/>
\r
1131 <taxon idref="236_Swine_H1N1_UnitedKingdom_1996"/>
\r
1135 <taxon idref="225_Swine_H1N1_UnitedKingdom_1993"/>
\r
1139 <taxon idref="212_Swine_H1N1_UnitedKingdom_1999"/>
\r
1143 <taxon idref="246_Swine_H1N1_UnitedKingdom_1994"/>
\r
1147 <taxon idref="211_Swine_H1N1_UnitedKingdom_1998"/>
\r
1151 <taxon idref="247_Swine_H1N1_UnitedKingdom_1997"/>
\r
1155 <taxon idref="141_Swine_H1N1_Italy_1997"/>
\r
1159 <taxon idref="123_Swine_H1N1_Italy_1996"/>
\r
1163 <taxon idref="140_Swine_H1N1_Italy_1998"/>
\r
1167 <taxon idref="191_Swine_H1N1_Italy_1997"/>
\r
1171 <taxon idref="310_Swine_H1N1_Germany_1993"/>
\r
1175 <taxon idref="228_Swine_H1N1_Denmark_1993"/>
\r
1179 <taxon idref="305_Swine_H1N1_Belgium_1998"/>
\r
1183 <taxon idref="168_Swine_H1N1_Spain_2003"/>
\r
1187 <taxon idref="159_Swine_H1N1_Spain_2004"/>
\r
1191 <taxon idref="278_Swine_H1N1_Hungary_2006"/>
\r
1195 <taxon idref="124_Swine_H1N1_France_1999"/>
\r
1199 <taxon idref="304_Swine_H1N1_China_2007"/>
\r
1203 <taxon idref="287_Swine_H1N1_Germany_2003"/>
\r
1207 <taxon idref="167_Swine_H1N1_Spain_2003"/>
\r
1211 <taxon idref="192_Swine_H1N2_Germany_2000"/>
\r
1215 <taxon idref="1_Human_H1N1_USA_1918"/>
\r
1219 <taxon idref="3_Human_H1N1_UnitedKingdom_1933"/>
\r
1223 <taxon idref="2_Human_H1N1_UnitedKingdom_1933"/>
\r
1227 <taxon idref="23_Human_H1_Japan_1967"/>
\r
1231 <taxon idref="7_Human_H1N1_Australia_1935"/>
\r
1235 <taxon idref="6_Human_H1N1_USA_1935"/>
\r
1239 <taxon idref="8_Human_H1N1_1936"/>
\r
1243 <taxon idref="4_Human_H1N1_PuertoRico_1934"/>
\r
1247 <taxon idref="5_Human_H1N1_PuertoRico_1934"/>
\r
1251 <taxon idref="10_Human_H1N1_USA_1942"/>
\r
1255 <taxon idref="11_Human_H1N1_USA_1943"/>
\r
1259 <taxon idref="12_Human_H1N1_USA_1943"/>
\r
1263 <taxon idref="13_Human_H1N1_USA_1945"/>
\r
1267 <taxon idref="9_Human_H1N1_USA_1940"/>
\r
1271 <taxon idref="14_Human_H1N1_1946"/>
\r
1275 <taxon idref="15_Human_H1N1_USA_1947"/>
\r
1279 <taxon idref="16_Human_H1N1_USA_1947"/>
\r
1283 <taxon idref="18_Human_H1N1_USA_1950"/>
\r
1287 <taxon idref="22_Human_H1N1_USA_1957"/>
\r
1291 <taxon idref="19_Human_H1N1_USA_1951"/>
\r
1295 <taxon idref="20_Human_H1N1_Malaysia_1954"/>
\r
1299 <taxon idref="17_Human_H1N1_USA_1948"/>
\r
1303 <taxon idref="21_Human_H1N1_Russia_1954"/>
\r
1307 <taxon idref="26_Human_H1N1_HongKong_1977_1954"/>
\r
1311 <taxon idref="27_Human_H1N1_USA_1978_1955"/>
\r
1315 <taxon idref="31_Human_H1N1_USA_1983_1960"/>
\r
1319 <taxon idref="29_Human_H1N1_UnitedKingdom_1982_1959"/>
\r
1323 <taxon idref="30_Human_H1N1_Fiji_1983_1960"/>
\r
1327 <taxon idref="28_Human_H1N1_India_1980_1957"/>
\r
1331 <taxon idref="33_Human_H1N1_USA_1986_1963"/>
\r
1335 <taxon idref="36_Human_H1N1_Italy_1989_1966"/>
\r
1339 <taxon idref="39_Human_H1N1_Mongolia_1991_1968"/>
\r
1343 <taxon idref="35_Human_H1N1_Japan_1989_1966"/>
\r
1347 <taxon idref="37_Human_H1N1_Italy_1989_1966"/>
\r
1351 <taxon idref="38_Human_H1N1_USA_1991_1968"/>
\r
1355 <taxon idref="44_Human_H1N1_USA_1995_1972"/>
\r
1359 <taxon idref="43_Human_H1N1_Switzerland_1995_1972"/>
\r
1363 <taxon idref="55_Human_H1N1_Australia_2000_1977"/>
\r
1367 <taxon idref="41_Human_H1N1_USA_1995_1972"/>
\r
1371 <taxon idref="48_Human_H1N1_Taiwan_1996_1973"/>
\r
1375 <taxon idref="42_Human_H1N1_China_1995_1972"/>
\r
1379 <taxon idref="45_Human_H1N1_USA_1995_1972"/>
\r
1383 <taxon idref="47_Human_H1N1_USA_1996_1973"/>
\r
1387 <taxon idref="40_Human_H1N1_China_1995_1972"/>
\r
1391 <taxon idref="46_Human_H1N1_China_1996_1973"/>
\r
1395 <taxon idref="52_Human_H1N1_HongKong_1998_1975"/>
\r
1399 <taxon idref="49_Human_H1N1_Taiwan_1997_1974"/>
\r
1403 <taxon idref="51_Human_H1N1_HongKong_1998_1975"/>
\r
1407 <taxon idref="50_Human_H1N1_HongKong_1998_1975"/>
\r
1411 <taxon idref="60_Human_H1N1_Taiwan_2002_1979"/>
\r
1415 <taxon idref="54_Human_H1N1_NewCaledonia_1999_1976"/>
\r
1419 <taxon idref="53_Human_H1N1_Taiwan_1999_1976"/>
\r
1423 <taxon idref="56_Human_H1N1_USA_2000_1977"/>
\r
1427 <taxon idref="57_Human_H1N1_NewZealand_2000_1977"/>
\r
1431 <taxon idref="58_Human_H1N1_NewZealand_2000_1977"/>
\r
1435 <taxon idref="61_Human_H1N2_USA_2002_1979"/>
\r
1439 <taxon idref="62_Human_H1N2_Denmark_2003_1980"/>
\r
1443 <taxon idref="64_Human_H1N2_USA_2003_1980"/>
\r
1447 <taxon idref="59_Human_H1N1_Japan_2001_1978"/>
\r
1451 <taxon idref="63_Human_H1N1_USA_2003_1980"/>
\r
1455 <taxon idref="65_Human_H1N1_Denmark_2004_1981"/>
\r
1459 <taxon idref="68_Human_H1N1_Australia_2005_1982"/>
\r
1463 <taxon idref="79_Human_H1N1_USA_2007_1984"/>
\r
1467 <taxon idref="76_Human_H1N1_USA_2006_1983"/>
\r
1471 <taxon idref="82_Human_H1N1_USA_2007_1984"/>
\r
1475 <taxon idref="72_Human_H1N1_Thailand_2006_1983"/>
\r
1479 <taxon idref="77_Human_H1N1_SolomonIslands_2006_1983"/>
\r
1483 <taxon idref="74_Human_H1N1_China_2006_1983"/>
\r
1487 <taxon idref="75_Human_H1N1_China_2006_1983"/>
\r
1491 <taxon idref="81_Human_H1N1_USA_2007_1984"/>
\r
1495 <taxon idref="71_Human_H1N1_China_2006_1983"/>
\r
1499 <taxon idref="73_Human_H1N1_China_2006_1983"/>
\r
1503 <taxon idref="98_Human_H1N1_USA_2008_1985"/>
\r
1507 <taxon idref="83_Human_H1N1_USA_2007_1984"/>
\r
1511 <taxon idref="84_Human_H1N1_USA_2007_1984"/>
\r
1515 <taxon idref="67_Human_H1N1_NewZealand_2004_1981"/>
\r
1519 <taxon idref="97_Human_H1N1_Australia_2008_1985"/>
\r
1523 <taxon idref="78_Human_H1N1_USA_2006_1983"/>
\r
1527 <taxon idref="80_Human_H1N1_USA_2007_1984"/>
\r
1531 <taxon idref="86_Human_H1N1_USA_2007_1984"/>
\r
1535 <taxon idref="92_Human_H1N1_USA_2008_1985"/>
\r
1539 <taxon idref="87_Human_H1N1_USA_2007_1984"/>
\r
1543 <taxon idref="88_Human_H1N1_USA_2007_1984"/>
\r
1547 <taxon idref="85_Human_H1N1_USA_2007_1984"/>
\r
1551 <taxon idref="95_Human_H1N1_USA_2008_1985"/>
\r
1555 <taxon idref="89_Human_H1N1_USA_2007_1984"/>
\r
1559 <taxon idref="93_Human_H1N1_USA_2008_1985"/>
\r
1563 <taxon idref="94_Human_H1N1_USA_2008_1985"/>
\r
1567 <taxon idref="96_Human_H1N1_USA_2008_1985"/>
\r
1571 <taxon idref="90_Human_H1N1_USA_2008_1985"/>
\r
1575 <taxon idref="100_Human_H1N1_USA_2008_1985"/>
\r
1579 <taxon idref="91_Human_H1N1_USA_2008_1985"/>
\r
1583 <taxon idref="99_Human_H1N1_USA_2008_1985"/>
\r
1587 <taxon idref="115_Swine_H1N1_USA_1930"/>
\r
1591 <taxon idref="166_Swine_H1N1_1931"/>
\r
1595 <taxon idref="292_Swine_H1N1_USA_1945"/>
\r
1599 <taxon idref="243_Swine_H1N1_USA_1942"/>
\r
1603 <taxon idref="244_Swine_H1N1_USA_1935"/>
\r
1607 <taxon idref="232_Swine_H1N1_USA_1957"/>
\r
1611 <taxon idref="104_Swine_H1N1_USA_1961"/>
\r
1615 <taxon idref="293_Swine_H1N1_USA_1968"/>
\r
1619 <taxon idref="219_Swine_H1N1_USA_1966"/>
\r
1623 <taxon idref="207_Swine_H1N1_USA_1967"/>
\r
1627 <taxon idref="190_Swine_H1N1_USA_1970"/>
\r
1631 <taxon idref="188_Swine_H1N1_USA_1971"/>
\r
1635 <taxon idref="257_Swine_H1N1_USA_1973"/>
\r
1639 <taxon idref="202_Swine_H1N1_USA_1975"/>
\r
1643 <taxon idref="308_Swine_H1N1_USA_1976"/>
\r
1647 <taxon idref="171_Swine_H1N1_USA_1977"/>
\r
1651 <taxon idref="240_Swine_H1N1_USA_1977"/>
\r
1655 <taxon idref="217_Swine_H1N1_USA_1977"/>
\r
1659 <taxon idref="242_Swine_H1N1_USA_1977"/>
\r
1663 <taxon idref="214_Swine_H1N1_USA_1976"/>
\r
1667 <taxon idref="170_Swine_H1N1_USA_1976"/>
\r
1671 <taxon idref="178_Swine_H1N1_USA_1977"/>
\r
1675 <taxon idref="205_Swine_H1N1_USA_1977"/>
\r
1679 <taxon idref="184_Swine_H1N1_USA_1977"/>
\r
1683 <taxon idref="187_Swine_H1N1_USA_1978"/>
\r
1687 <taxon idref="144_Swine_H1N1_Japan_1977"/>
\r
1691 <taxon idref="290_Swine_H1N1_UnitedKingdom_1993"/>
\r
1695 <taxon idref="312_Swine_H1N1_UnitedKingdom_1986"/>
\r
1699 <taxon idref="103_Swine_H1N1_Japan_1979"/>
\r
1703 <taxon idref="113_Swine_H1N2_Japan_1996"/>
\r
1707 <taxon idref="110_Swine_H1N2_Japan_2003"/>
\r
1711 <taxon idref="128_Swine_H1N2_Japan_2006"/>
\r
1715 <taxon idref="183_Swine_H1N1_USA_1976"/>
\r
1719 <taxon idref="209_Swine_H1N1_USA_1978"/>
\r
1723 <taxon idref="231_Swine_H1N1_USA_1977"/>
\r
1727 <taxon idref="127_Swine_H1N2_Japan_1980"/>
\r
1731 <taxon idref="145_Swine_H1N1_Japan_1981"/>
\r
1735 <taxon idref="215_Swine_H1N1_USA_1976"/>
\r
1739 <taxon idref="218_Swine_H1N1_USA_1977"/>
\r
1743 <taxon idref="221_Swine_H1N1_USA_1978"/>
\r
1747 <taxon idref="208_Swine_H1N1_USA_1978"/>
\r
1751 <taxon idref="220_Swine_H1N1_USA_1978"/>
\r
1755 <taxon idref="112_Swine_H1N2_Thailand_2005"/>
\r
1759 <taxon idref="261_Swine_H1N1_Thailand_2005"/>
\r
1763 <taxon idref="143_Swine_H1N1_Thailand_2004"/>
\r
1767 <taxon idref="262_Swine_H1N1_Thailand_2005"/>
\r
1771 <taxon idref="206_Swine_H1N1_USA_1980"/>
\r
1775 <taxon idref="186_Swine_H1N1_USA_1979"/>
\r
1779 <taxon idref="189_Swine_H1N1_USA_1980"/>
\r
1783 <taxon idref="203_Swine_H1N1_Canada_1981"/>
\r
1787 <taxon idref="216_Swine_H1N1_Canada_1981"/>
\r
1791 <taxon idref="222_Swine_H1N1_USA_1987"/>
\r
1795 <taxon idref="299_Swine_H1N1_USA_1992"/>
\r
1799 <taxon idref="268_Swine_H1N1_Canada_2004"/>
\r
1803 <taxon idref="281_Swine_H1N1_Canada_2003"/>
\r
1807 <taxon idref="253_Swine_H1N1_Canada_2004"/>
\r
1811 <taxon idref="301_Swine_H1_Canada_1991"/>
\r
1815 <taxon idref="194_Swine_H1N2_Taiwan_2003"/>
\r
1819 <taxon idref="282_Swine_H1N2_Taiwan_2004"/>
\r
1823 <taxon idref="249_Swine_H1N1_Canada_2003"/>
\r
1827 <taxon idref="251_Swine_H1N1_Canada_2003"/>
\r
1831 <taxon idref="245_Swine_H1N1_USA_1986"/>
\r
1835 <taxon idref="185_Swine_H1N1_USA_1985"/>
\r
1839 <taxon idref="230_Swine_H1N1_USA_1987"/>
\r
1843 <taxon idref="142_Swine_H1N1_Thailand_2000"/>
\r
1847 <taxon idref="118_Swine_H1N1_USA_1997"/>
\r
1851 <taxon idref="175_Swine_H1N2_USA_2001"/>
\r
1855 <taxon idref="300_Swine_H1N1_USA_1988"/>
\r
1859 <taxon idref="111_Swine_H1N1_Thailand_2003"/>
\r
1863 <taxon idref="241_Swine_H1N1_USA_1988"/>
\r
1867 <taxon idref="201_Swine_H1N1_USA_1988"/>
\r
1871 <taxon idref="239_Swine_H1N1_China_2001"/>
\r
1875 <taxon idref="294_Swine_H1N1_China_2005"/>
\r
1879 <taxon idref="204_Swine_H1N1_USA_1991"/>
\r
1883 <taxon idref="136_Swine_H1N1_USA_1997"/>
\r
1887 <taxon idref="108_Swine_H1N1_USA_1997"/>
\r
1891 <taxon idref="109_Swine_H1N1_USA_1998"/>
\r
1895 <taxon idref="146_Swine_H1N1_USA_1998"/>
\r
1899 <taxon idref="280_Swine_H1N2_China_2004"/>
\r
1903 <taxon idref="284_Swine_H1N2_China_2005"/>
\r
1907 <taxon idref="306_Swine_H1N2_China_2007"/>
\r
1911 <taxon idref="271_Swine_H1N1_USA_1999"/>
\r
1915 <taxon idref="148_Swine_H1N2_USA_2000"/>
\r
1919 <taxon idref="138_Swine_H1N2_USA_2001"/>
\r
1923 <taxon idref="272_Swine_H1N1_USA_2002"/>
\r
1927 <taxon idref="172_Swine_H1N2_USA_2001"/>
\r
1931 <taxon idref="120_Swine_H1N2_USA_2001"/>
\r
1935 <taxon idref="193_Swine_H1N2_SouthKorea_2002"/>
\r
1939 <taxon idref="160_Swine_H1N2_USA_2001"/>
\r
1943 <taxon idref="260_Swine_H1N1_USA_2004"/>
\r
1947 <taxon idref="296_Swine_H1N1_SouthKorea_2004"/>
\r
1951 <taxon idref="297_Swine_H1N1_SouthKorea_2005"/>
\r
1955 <taxon idref="174_Swine_H1N2_USA_2001"/>
\r
1959 <taxon idref="147_Swine_H1N2_USA_2001"/>
\r
1963 <taxon idref="258_Swine_H1N2_USA_2001"/>
\r
1967 <taxon idref="139_Swine_H1N2_USA_2000"/>
\r
1971 <taxon idref="101_Human_H1N1_USA_2009"/>
\r
1975 <taxon idref="313_Human_H1N1_USA_2009"/>
\r
1979 <taxon idref="269_Swine_H1N2_China_2006"/>
\r
1983 <taxon idref="283_Swine_H1N2_China_2005"/>
\r
1987 <taxon idref="119_Swine_H1N2_USA_1999"/>
\r
1991 <taxon idref="173_Swine_H1N2_USA_2001"/>
\r
1995 <taxon idref="121_Swine_H1N2_USA_2001"/>
\r
1999 <taxon idref="122_Swine_H1N2_USA_2001"/>
\r
2003 <taxon idref="137_Swine_H1N2_USA_2001"/>
\r
2007 <taxon idref="263_Swine_H1N1_USA_2007"/>
\r
2011 <taxon idref="273_Swine_H1N2_USA_2003"/>
\r
2015 <taxon idref="151_Swine_H1N2_USA_2001"/>
\r
2019 <taxon idref="259_Swine_H1N2_USA_2004"/>
\r
2023 <taxon idref="291_Swine_H1N2_SouthKorea_2005"/>
\r
2027 <taxon idref="266_Swine_H1N2_SouthKorea_2005"/>
\r
2031 <taxon idref="298_Swine_H1N2_SouthKorea_2005"/>
\r
2035 <taxon idref="265_Swine_H1N2_SouthKorea_2004"/>
\r
2039 <taxon idref="275_Swine_H1N2_SouthKorea_2006"/>
\r
2044 <!-- The unique patterns from 1 to end -->
\r
2045 <!-- npatterns=1136 -->
\r
2046 <patterns id="patterns" from="1" strip="false">
\r
2047 <alignment idref="alignment"/>
\r
2050 <!-- A prior assumption that the population size has remained constant -->
\r
2051 <!-- throughout the time spanned by the genealogy. -->
\r
2052 <constantSize id="constant" units="years">
\r
2054 <parameter id="constant.popSize" value="1.0" lower="0.0"/>
\r
2058 <!-- Construct a rough-and-ready UPGMA tree as an starting tree -->
\r
2059 <upgmaTree id="startingTree" rootHeight="200.0">
\r
2060 <distanceMatrix correction="JC">
\r
2063 <!-- To generate UPGMA starting tree, only use the 1st aligment, which may be 1 of many aligments using this tree.-->
\r
2064 <alignment idref="alignment"/>
\r
2069 <!-- Generate a tree model -->
\r
2070 <treeModel id="treeModel">
\r
2071 <upgmaTree idref="startingTree"/>
\r
2073 <parameter id="treeModel.rootHeight"/>
\r
2075 <nodeHeights internalNodes="true">
\r
2076 <parameter id="treeModel.internalNodeHeights"/>
\r
2078 <nodeHeights internalNodes="true" rootNode="true">
\r
2079 <parameter id="treeModel.allInternalNodeHeights"/>
\r
2083 <!-- Generate a coalescent likelihood -->
\r
2084 <coalescentLikelihood id="coalescent">
\r
2086 <constantSize idref="constant"/>
\r
2089 <treeModel idref="treeModel"/>
\r
2091 </coalescentLikelihood>
\r
2093 <!-- The uncorrelated relaxed clock (Drummond, Ho, Phillips & Rambaut (2006) PLoS Biology 4, e88 )-->
\r
2094 <discretizedBranchRates id="branchRates">
\r
2095 <treeModel idref="treeModel"/>
\r
2097 <logNormalDistributionModel meanInRealSpace="true">
\r
2099 <parameter id="ucld.mean" value="1.0" lower="0.0"/>
\r
2102 <parameter id="ucld.stdev" value="0.3333333333333333" lower="0.0"/>
\r
2104 </logNormalDistributionModel>
\r
2107 <parameter id="branchRates.categories"/>
\r
2109 </discretizedBranchRates>
\r
2110 <rateStatistic id="meanRate" name="meanRate" mode="mean" internal="true" external="true">
\r
2111 <treeModel idref="treeModel"/>
\r
2112 <discretizedBranchRates idref="branchRates"/>
\r
2114 <rateStatistic id="coefficientOfVariation" name="coefficientOfVariation" mode="coefficientOfVariation" internal="true" external="true">
\r
2115 <treeModel idref="treeModel"/>
\r
2116 <discretizedBranchRates idref="branchRates"/>
\r
2118 <rateCovarianceStatistic id="covariance" name="covariance">
\r
2119 <treeModel idref="treeModel"/>
\r
2120 <discretizedBranchRates idref="branchRates"/>
\r
2121 </rateCovarianceStatistic>
\r
2123 <!-- The HKY substitution model (Hasegawa, Kishino & Yano, 1985) -->
\r
2124 <HKYModel id="hky">
\r
2126 <frequencyModel dataType="nucleotide">
\r
2127 <alignment idref="alignment"/>
\r
2129 <parameter id="frequencies" dimension="4"/>
\r
2134 <parameter id="kappa" value="2.0" lower="0.0"/>
\r
2138 <!-- site model -->
\r
2139 <siteModel id="siteModel">
\r
2140 <substitutionModel>
\r
2141 <HKYModel idref="hky"/>
\r
2142 </substitutionModel>
\r
2143 <gammaShape gammaCategories="5">
\r
2144 <parameter id="alpha" value="0.5" lower="0.0"/>
\r
2148 <!-- Likelihood for tree given sequence data -->
\r
2149 <treeLikelihood id="treeLikelihood" useAmbiguities="false" stateTagName="states">
\r
2150 <patterns idref="patterns"/>
\r
2151 <treeModel idref="treeModel"/>
\r
2152 <siteModel idref="siteModel"/>
\r
2153 <discretizedBranchRates idref="branchRates"/>
\r
2156 <!-- Define operators -->
\r
2157 <operators id="operators">
\r
2158 <scaleOperator scaleFactor="0.75" weight="0.1">
\r
2159 <parameter idref="kappa"/>
\r
2161 <scaleOperator scaleFactor="0.75" weight="0.1">
\r
2162 <parameter idref="alpha"/>
\r
2164 <scaleOperator scaleFactor="0.75" weight="3">
\r
2165 <parameter idref="ucld.mean"/>
\r
2167 <scaleOperator scaleFactor="0.75" weight="3">
\r
2168 <parameter idref="ucld.stdev"/>
\r
2170 <subtreeSlide size="0.1" gaussian="true" weight="15">
\r
2171 <treeModel idref="treeModel"/>
\r
2173 <narrowExchange weight="15">
\r
2174 <treeModel idref="treeModel"/>
\r
2176 <wideExchange weight="3">
\r
2177 <treeModel idref="treeModel"/>
\r
2179 <wilsonBalding weight="3">
\r
2180 <treeModel idref="treeModel"/>
\r
2182 <scaleOperator scaleFactor="0.75" weight="3">
\r
2183 <parameter idref="treeModel.rootHeight"/>
\r
2185 <uniformOperator weight="30">
\r
2186 <parameter idref="treeModel.internalNodeHeights"/>
\r
2187 </uniformOperator>
\r
2188 <scaleOperator scaleFactor="0.75" weight="3">
\r
2189 <parameter idref="constant.popSize"/>
\r
2191 <upDownOperator scaleFactor="0.75" weight="3">
\r
2193 <parameter idref="ucld.mean"/>
\r
2196 <parameter idref="treeModel.allInternalNodeHeights"/>
\r
2199 <swapOperator size="1" weight="10" autoOptimize="false">
\r
2200 <parameter idref="branchRates.categories"/>
\r
2202 <uniformIntegerOperator weight="10">
\r
2203 <parameter idref="branchRates.categories"/>
\r
2204 </uniformIntegerOperator>
\r
2207 <!-- Define MCMC -->
\r
2208 <mcmc id="mcmc" chainLength="100000000" autoOptimize="true">
\r
2209 <posterior id="posterior">
\r
2210 <prior id="prior">
\r
2211 <gammaPrior shape="2.0" scale="1.0" offset="0.0">
\r
2212 <parameter idref="kappa"/>
\r
2214 <gammaPrior shape="2.0" scale="0.25" offset="0.0">
\r
2215 <parameter idref="alpha"/>
\r
2217 <gammaPrior shape="4.0" scale="20" offset="0.0">
\r
2218 <parameter idref="ucld.stdev"/>
\r
2220 <gammaPrior shape="2.0" scale="0.001" offset="0.0">
\r
2221 <parameter idref="ucld.mean"/>
\r
2224 <uniformPrior lower="100.0" upper="500.0">
\r
2225 <parameter idref="treeModel.rootHeight"/>
\r
2228 <exponentialPrior mean="1.0" offset="0.0">
\r
2229 <parameter idref="constant.popSize"/>
\r
2230 </exponentialPrior>
\r
2231 <coalescentLikelihood idref="coalescent"/>
\r
2233 <likelihood id="likelihood">
\r
2234 <treeLikelihood idref="treeLikelihood"/>
\r
2237 <operators idref="operators"/>
\r
2239 <!-- write log to screen -->
\r
2240 <log id="screenLog" logEvery="10000">
\r
2241 <column label="Posterior" dp="4" width="12">
\r
2242 <posterior idref="posterior"/>
\r
2244 <column label="Prior" dp="4" width="12">
\r
2245 <prior idref="prior"/>
\r
2247 <column label="Likelihood" dp="4" width="12">
\r
2248 <likelihood idref="likelihood"/>
\r
2250 <column label="rootHeight" sf="6" width="12">
\r
2251 <parameter idref="treeModel.rootHeight"/>
\r
2253 <column label="ucld.mean" sf="6" width="12">
\r
2254 <parameter idref="ucld.mean"/>
\r
2258 <!-- write log to file -->
\r
2259 <log id="fileLog" logEvery="10000" fileName="H1.Beast.log" overwrite="false">
\r
2260 <posterior idref="posterior"/>
\r
2261 <prior idref="prior"/>
\r
2262 <likelihood idref="likelihood"/>
\r
2263 <parameter idref="treeModel.rootHeight"/>
\r
2264 <parameter idref="constant.popSize"/>
\r
2265 <parameter idref="kappa"/>
\r
2266 <parameter idref="alpha"/>
\r
2267 <parameter idref="ucld.mean"/>
\r
2268 <parameter idref="ucld.stdev"/>
\r
2269 <rateStatistic idref="meanRate"/>
\r
2270 <rateStatistic idref="coefficientOfVariation"/>
\r
2271 <rateCovarianceStatistic idref="covariance"/>
\r
2272 <treeLikelihood idref="treeLikelihood"/>
\r
2273 <coalescentLikelihood idref="coalescent"/>
\r
2276 <!-- write tree log to file -->
\r
2277 <logTree id="treeFileLog" logEvery="10000" nexusFormat="true" fileName="H1.Beast.trees" sortTranslationTable="true">
\r
2278 <treeModel idref="treeModel"/>
\r
2279 <trait name="rate" tag="rate">
\r
2280 <discretizedBranchRates idref="branchRates"/>
\r
2282 <posterior idref="posterior"/>
\r
2286 <property name="timer">
\r
2287 <mcmc idref="mcmc"/>
\r