# HG changeset patch
# User iuc
# Date 1581624207 18000
# Node ID d02c8e6f7f2ad855946ace5e24f2d466d81ffdf0
# Parent 7b3f9c78cf6d14bdd3fe3bbcbc3f12d184aae3ad
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
diff -r 7b3f9c78cf6d -r d02c8e6f7f2a hyphy_meme.xml
--- a/hyphy_meme.xml Wed Aug 21 12:26:38 2019 -0400
+++ b/hyphy_meme.xml Thu Feb 13 15:03:27 2020 -0500
@@ -37,6 +37,10 @@
10.1371/journal.pgen.1002764
diff -r 7b3f9c78cf6d -r d02c8e6f7f2a macros.xml
--- a/macros.xml Wed Aug 21 12:26:38 2019 -0400
+++ b/macros.xml Thu Feb 13 15:03:27 2020 -0500
@@ -72,7 +72,7 @@
- 2.5.0
+ 2.5.2
diff -r 7b3f9c78cf6d -r d02c8e6f7f2a test-data/bgm-out1.json
--- a/test-data/bgm-out1.json Wed Aug 21 12:26:38 2019 -0400
+++ b/test-data/bgm-out1.json Thu Feb 13 15:03:27 2020 -0500
@@ -1,282 +1,42 @@
{
"MLE":{
"content": [
-[3, 4, 0.01806536842133838, 0.0196151052739404, 0.03768047369527878, 2, 4, 1],
- [3, 5, 0.0136689326165866, 0.08411879896894461, 0.09778773158553121, 2, 2, 1],
- [3, 6, 0.01626880980001384, 0.05621779910581199, 0.07248660890582583, 2, 2, 1],
- [3, 7, 0.01296085994820069, 0.02206081801264715, 0.03502167796084783, 2, 1, 0],
- [3, 9, 0.01069476203525126, 0.01376808584576788, 0.02446284788101914, 2, 3, 0],
- [3, 10, 0.05465425513197631, 0.1433115560788012, 0.1979658112107776, 2, 1, 1],
- [3, 11, 0.02893963856420952, 0.01605584764833427, 0.04499548621254379, 2, 1, 0],
- [3, 12, 0.01072516405613842, 0.0249434485528662, 0.03566861260900463, 2, 1, 0],
- [3, 14, 0.02105948857071199, 0.05408645518169206, 0.07514594375240405, 2, 2, 1],
- [3, 15, 0.0123000231875007, 0.02432900062064017, 0.03662902380814088, 2, 3, 1],
- [3, 16, 0.005326227185235535, 0.02715178476956077, 0.0324780119547963, 2, 4, 1],
- [3, 17, 0.03377277022598092, 0.04443847194728315, 0.07821124217326408, 2, 2, 1],
- [3, 18, 0.01498654024671119, 0.01399705284721538, 0.02898359309392656, 2, 2, 0],
- [3, 20, 0.03160117895292701, 0.03379356385898681, 0.06539474281191382, 2, 3, 1],
- [3, 21, 0.005825814343840907, 0.01762290041418722, 0.02344871475802813, 2, 5, 1],
- [3, 22, 0.004808842565391303, 0.01857986311191453, 0.02338870567730583, 2, 5, 1],
- [3, 23, 0.01560225549428971, 0.01369335589628938, 0.02929561139057909, 2, 3, 0],
- [3, 24, 0.02796792379060828, 0.0120172661798151, 0.03998518997042338, 2, 2, 0],
- [3, 25, 0.004879890854338218, 0.05174659736268138, 0.05662648821701959, 2, 3, 1],
- [3, 26, 0.008542556433088364, 0.02342067235707167, 0.03196322879016003, 2, 1, 0],
- [3, 28, 0.02842598870361674, 0.04882702442678508, 0.07725301313040182, 2, 2, 1],
- [3, 29, 0.02983611705240465, 0.04834281650968934, 0.07817893356209399, 2, 2, 1],
- [3, 30, 0.02136530753356511, 0.056551049600131, 0.0779163571336961, 2, 2, 1],
- [4, 5, 0.04128639081201998, 0.1643521228119713, 0.2056385136239913, 4, 2, 2],
- [4, 6, 0.002891680521324363, 0.02014100082658794, 0.0230326813479123, 4, 2, 1],
- [4, 7, 0.01937071123900217, 0.03955420345740617, 0.05892491469640834, 4, 1, 1],
- [4, 9, 0.005876622911646858, 0.01316366694762399, 0.01904028985927084, 4, 3, 1],
- [4, 10, 0.02063883956421052, 0.03235708509290364, 0.05299592465711416, 4, 1, 1],
- [4, 11, 0.05646705485150577, 0.03046422064113512, 0.08693127549264089, 4, 1, 1],
- [4, 12, 0.018550325874111, 0.04456585108483763, 0.06311617695894862, 4, 1, 1],
- [4, 14, 0.002644483178150749, 0.02400887432195999, 0.02665335750011074, 4, 2, 1],
- [4, 15, 0.01378625971212575, 0.03709407143284885, 0.05088033114497461, 4, 3, 2],
- [4, 16, 0.005366210549264398, 0.0254419855729714, 0.03080819612223579, 4, 4, 2],
- [4, 17, 0.08506807888824773, 0.08873474434715359, 0.1738028232354013, 4, 2, 2],
- [4, 18, 0.01666065271395927, 0.01550783907099662, 0.03216849178495589, 4, 2, 1],
- [4, 20, 0.0602710511807769, 0.03562465630098035, 0.09589570748175724, 4, 3, 2],
- [4, 21, 0.03064565490801606, 0.06355132795273535, 0.09419698286075141, 4, 5, 3],
- [4, 22, 0.02451199601165472, 0.07489768093572295, 0.09940967694737768, 4, 5, 3],
- [4, 23, 0.03630394203907011, 0.03058821944652209, 0.06689216148559221, 4, 3, 2],
- [4, 24, 0.02164778178638001, 0.008961778863845419, 0.03060956065022543, 4, 2, 0],
- [4, 25, 0.01168690527839325, 0.07747501344981376, 0.08916191872820702, 4, 3, 2],
- [4, 26, 0.01588288283660194, 0.04096522221306678, 0.05684810504966872, 4, 1, 1],
- [4, 28, 0.01128665086452497, 0.01582662360389917, 0.02711327446842414, 4, 2, 1],
- [4, 29, 0.01028593387764938, 0.01547886135935664, 0.02576479523700602, 4, 2, 1],
- [4, 30, 0.004517730197507495, 0.02179721676324585, 0.02631494696075334, 4, 2, 1],
- [5, 6, 0.01349845941886215, 0.0271001713778612, 0.04059863079672335, 2, 2, 1],
- [5, 7, 0.08386293017699854, 0.05547962590044048, 0.139342556077439, 2, 1, 1],
- [5, 9, 0.01976650604639912, 0.01082947702714442, 0.03059598307354354, 2, 3, 1],
- [5, 10, 0.08663121746727073, 0.05454639965761584, 0.1411776171248866, 2, 1, 1],
- [5, 11, 0.03770763685855846, 0.006284585998205416, 0.04399222285676388, 2, 1, 0],
- [5, 12, 0.1076906900926125, 0.0473111213301104, 0.1550018114227228, 2, 1, 1],
- [5, 14, 0.01972942054521223, 0.0320506800558711, 0.05178010060108334, 2, 2, 1],
- [5, 15, 0.0115296223772864, 0.009425622068293078, 0.02095524444557947, 2, 3, 1],
- [5, 16, 0.05795468769109502, 0.07437721131546923, 0.1323318990065643, 2, 4, 2],
- [5, 17, 0.04893957970901563, 0.01779579930892645, 0.06673537901794209, 2, 2, 1],
- [5, 18, 0.06914575237510151, 0.01277854849843139, 0.08192430087353289, 2, 2, 1],
- [5, 20, 0.04606204168737617, 0.008407721695554574, 0.05446976338293075, 2, 3, 1],
- [5, 21, 0.06137939961987368, 0.03626744029311923, 0.09764683991299292, 2, 5, 2],
- [5, 22, 0.04000126166279955, 0.03754521666039747, 0.07754647832319703, 2, 5, 2],
- [5, 23, 0.03357555220343731, 0.01381372812520867, 0.04738928032864598, 2, 3, 1],
- [5, 24, 0.03380670133572664, 0.003731548300121901, 0.03753824963584854, 2, 2, 0],
- [5, 25, 0.09004803803938788, 0.2417884826530335, 0.3318365206924214, 2, 3, 2],
- [5, 26, 0.08754942747826591, 0.05315050503462983, 0.1406999325128958, 2, 1, 1],
- [5, 28, 0.04567502066103889, 0.01808010305875397, 0.06375512371979286, 2, 2, 1],
- [5, 29, 0.03260950473238529, 0.02317187888808829, 0.05578138362047358, 2, 2, 1],
- [5, 30, 0.02112358475746083, 0.02897865767093947, 0.05010224242840029, 2, 2, 1],
- [6, 7, 0.01668462680139263, 0.009946683404740683, 0.02663131020613331, 2, 1, 0],
- [6, 9, 0.01988584439856818, 0.009045415077913333, 0.02893125947648151, 2, 3, 1],
- [6, 10, 0.07997756465918539, 0.02777823877936857, 0.107755803438554, 2, 1, 1],
- [6, 11, 0.0427529051299776, 0.004277233013937032, 0.04703013814391463, 2, 1, 0],
- [6, 12, 0.01457894161504904, 0.0107389078090505, 0.02531784942409954, 2, 1, 0],
- [6, 14, 0.2325712692000255, 0.2014841220660465, 0.4340553912660721, 2, 2, 2],
- [6, 15, 0.1692106649881499, 0.05297107692530162, 0.2221817419134515, 2, 3, 2],
- [6, 16, 0.05738158701493928, 0.04589333277643135, 0.1032749197913706, 2, 4, 2],
- [6, 17, 0.04815193631537981, 0.009529021235036772, 0.05768095755041659, 2, 2, 1],
- [6, 18, 0.01912767387535096, 0.002044170024231443, 0.0211718438995824, 2, 2, 0],
- [6, 20, 0.02061887763751207, 0.004752091964805672, 0.02537096960231774, 2, 3, 0],
- [6, 21, 0.04247087838195826, 0.02528613276636166, 0.06775701114831992, 2, 5, 2],
- [6, 22, 0.04642062375115955, 0.02142488295951156, 0.06784550671067111, 2, 5, 2],
- [6, 23, 0.01554561721459279, 0.006425146203498221, 0.02197076341809101, 2, 3, 0],
- [6, 24, 0.03314786253017613, 0.001917115026076292, 0.03506497755625242, 2, 2, 0],
- [6, 25, 0.0940662182949361, 0.1384869187847857, 0.2325531370797218, 2, 3, 2],
- [6, 26, 0.01345296901600206, 0.004879799683521298, 0.01833276869952336, 2, 1, 0],
- [6, 28, 0.03796224039722292, 0.007515605266225617, 0.04547784566344854, 2, 2, 1],
- [6, 29, 0.05130583555953379, 0.01021357548333445, 0.06151941104286825, 2, 2, 1],
- [6, 30, 0.2318428453473779, 0.2372832334677343, 0.4691260788151123, 2, 2, 2],
- [7, 9, 0.04510729938504034, 0.033455377610294, 0.07856267699533434, 1, 3, 1],
- [7, 10, 0.01448672927711553, 0.01471180827475936, 0.0291985375518749, 1, 1, 0],
- [7, 11, 0.04558043072600854, 0.01092269815769229, 0.05650312888370083, 1, 1, 0],
- [7, 12, 0.180236004387841, 0.1473331361936553, 0.3275691405814962, 1, 1, 1],
- [7, 14, 0.004060491038913412, 0.009736071123258729, 0.01379656216217214, 1, 2, 0],
- [7, 15, 0.007246951454732821, 0.008020333839217355, 0.01526728529395018, 1, 3, 0],
- [7, 16, 0.02266593379543114, 0.02916472528901524, 0.05183065908444638, 1, 4, 1],
- [7, 17, 0.01353159955561796, 0.006519983350346921, 0.02005158290596488, 1, 2, 0],
- [7, 18, 0.1260783187676728, 0.05727101709727531, 0.1833493358649481, 1, 2, 1],
- [7, 20, 0.09497180416371181, 0.03920153451995714, 0.134173338683669, 1, 3, 1],
- [7, 21, 0.01391734233658772, 0.01774896716072902, 0.03166630949731674, 1, 5, 1],
- [7, 22, 0.01403403421609152, 0.02021415605799259, 0.03424819027408411, 1, 5, 1],
- [7, 23, 0.07875763940318095, 0.02839812636719212, 0.1071557657703731, 1, 3, 1],
- [7, 24, 0.04219288785522956, 0.006992293554900667, 0.04918518141013023, 1, 2, 0],
- [7, 25, 0.01888383639176133, 0.07660835994985157, 0.09549219634161291, 1, 3, 1],
- [7, 26, 0.1593820711044853, 0.1731736129027814, 0.3325556840072666, 1, 1, 1],
- [7, 28, 0.01379492231999666, 0.008854310031253648, 0.0226492323512503, 1, 2, 0],
- [7, 29, 0.01318267142576915, 0.01115280933551254, 0.02433548076128169, 1, 2, 0],
- [7, 30, 0.005464156565736539, 0.01604643247941549, 0.02151058904515203, 1, 2, 0],
- [9, 10, 0.008743328720289559, 0.008998664007820409, 0.01774199272810997, 3, 1, 0],
- [9, 11, 0.02301313307916227, 0.008353618087185346, 0.03136675116634761, 3, 1, 0],
- [9, 12, 0.03485480851874616, 0.0385220468500885, 0.07337685536883466, 3, 1, 1],
- [9, 14, 0.00925561597787489, 0.02345072843860894, 0.03270634441648383, 3, 2, 1],
- [9, 15, 0.005885707639577632, 0.0093457630141815, 0.01523147065375913, 3, 3, 1],
- [9, 16, 0.1352472349062049, 0.4258754197367833, 0.5611226546429883, 3, 4, 3],
- [9, 17, 0.0114528061541329, 0.009382339097390304, 0.0208351452515232, 3, 2, 0],
- [9, 18, 0.02851553908154206, 0.01525552104269379, 0.04377106012423586, 3, 2, 1],
- [9, 20, 0.01822901326926599, 0.01058740382851504, 0.02881641709778102, 3, 3, 1],
- [9, 21, 0.01637284646045184, 0.01528766975294247, 0.03166051621339431, 3, 5, 2],
- [9, 22, 0.01125203456673749, 0.01471364636147226, 0.02596568092820975, 3, 5, 2],
- [9, 23, 0.01581371454122383, 0.008723591174246868, 0.02453730571547069, 3, 3, 1],
- [9, 24, 0.04988705657909906, 0.01387214589279543, 0.06375920247189448, 3, 2, 1],
- [9, 25, 0.02481744876612966, 0.09561117569876813, 0.1204286244648978, 3, 3, 2],
- [9, 26, 0.02474648571293647, 0.05329817226044276, 0.07804465797337923, 3, 1, 1],
- [9, 28, 0.0133763748141426, 0.01726376204208423, 0.03064013685622684, 3, 2, 1],
- [9, 29, 0.01447958284562607, 0.02105672282873693, 0.03553630567436301, 3, 2, 1],
- [9, 30, 0.004787350233147937, 0.02258996514478861, 0.02737731537793655, 3, 2, 1],
- [10, 11, 0.04076687919145038, 0.01600339189308192, 0.05677027108453229, 1, 1, 0],
- [10, 12, 0.01487003942060377, 0.01285394941082142, 0.02772398883142518, 1, 1, 0],
- [10, 14, 0.0278020913930161, 0.06116723064367017, 0.08896932203668627, 1, 2, 1],
- [10, 15, 0.02590065104611214, 0.04413779140155937, 0.07003844244767152, 1, 3, 1],
- [10, 16, 0.01473871457697519, 0.03900854939746186, 0.05374726397443705, 1, 4, 1],
- [10, 17, 0.07737832850149316, 0.04512778545801077, 0.1225061139595039, 1, 2, 1],
- [10, 18, 0.01848975784724837, 0.00977696218399207, 0.02826672003124044, 1, 2, 0],
- [10, 20, 0.02248228077129723, 0.006391817662418776, 0.028874098433716, 1, 3, 0],
- [10, 21, 0.01548391498233171, 0.01956514936920832, 0.03504906435154003, 1, 5, 1],
- [10, 22, 0.01618209456972476, 0.02198162318745958, 0.03816371775718434, 1, 5, 1],
- [10, 23, 0.01304324890636816, 0.007815357572873324, 0.02085860647924148, 1, 3, 0],
- [10, 24, 0.03420490961110176, 0.008535296159903609, 0.04274020577100537, 1, 2, 0],
- [10, 25, 0.0147192856248153, 0.06581358768988828, 0.08053287331470357, 1, 3, 1],
- [10, 26, 0.01551389889619659, 0.02137375724421267, 0.03688765614040926, 1, 1, 0],
- [10, 28, 0.08242337980044148, 0.06924953639794011, 0.1516729161983816, 1, 2, 1],
- [10, 29, 0.0486391168101336, 0.06529494069867375, 0.1139340575088074, 1, 2, 1],
- [10, 30, 0.03219208960454593, 0.08832014266169741, 0.1205122322662433, 1, 2, 1],
- [11, 12, 0.0083422559528536, 0.04577125284234392, 0.05411350879519752, 1, 1, 0],
- [11, 14, 0.003063442830455156, 0.03058506004416841, 0.03364850287462357, 1, 2, 0],
- [11, 15, 0.008700688461801026, 0.02837240877883479, 0.03707309724063582, 1, 3, 0],
- [11, 16, 0.002513035135905159, 0.033081097723843, 0.03559413285974816, 1, 4, 0],
- [11, 17, 0.01015972517797896, 0.02585886367401776, 0.03601858885199673, 1, 2, 0],
- [11, 18, 0.01760510226017101, 0.02599830916230194, 0.04360341142247295, 1, 2, 0],
- [11, 20, 0.01570796171982357, 0.02432862307641051, 0.04003658479623408, 1, 3, 0],
- [11, 21, 0.005149376434442727, 0.02438894100547246, 0.02953831743991518, 1, 5, 0],
- [11, 22, 0.009744174308072966, 0.02717998704157922, 0.03692416134965219, 1, 5, 0],
- [11, 23, 0.0112816847864048, 0.02443013410042389, 0.0357118188868287, 1, 3, 0],
- [11, 24, 0.02611002944106307, 0.0243078721393825, 0.05041790158044557, 1, 2, 0],
- [11, 25, 0.00220817709319456, 0.04746832197244566, 0.04967649906564022, 1, 3, 0],
- [11, 26, 0.01079476529061294, 0.04998538352365951, 0.06078014881427245, 1, 1, 0],
- [11, 28, 0.007641379119979673, 0.03338702752077345, 0.04102840664075313, 1, 2, 0],
- [11, 29, 0.007824939016498385, 0.03557816199737629, 0.04340310101387468, 1, 2, 0],
- [11, 30, 0.002863447023878826, 0.03959507498879136, 0.04245852201267018, 1, 2, 0],
- [12, 14, 0.003531669272860574, 0.01503022692694298, 0.01856189619980356, 1, 2, 0],
- [12, 15, 0.005687502712301731, 0.009779382902868514, 0.01546688561517024, 1, 3, 0],
- [12, 16, 0.01897951429643458, 0.03338924626281588, 0.05236876055925047, 1, 4, 1],
- [12, 17, 0.01327573410150146, 0.008423500238909153, 0.02169923434041061, 1, 2, 0],
- [12, 18, 0.1492207326112999, 0.04435218220084611, 0.193572914812146, 1, 2, 1],
- [12, 20, 0.08617756897569587, 0.03342886351154893, 0.1196064324872448, 1, 3, 1],
- [12, 21, 0.01285874706488638, 0.01979657138334778, 0.03265531844823416, 1, 5, 1],
- [12, 22, 0.01379762818626092, 0.01723547685811808, 0.03103310504437899, 1, 5, 1],
- [12, 23, 0.06866921830001689, 0.0301984941528498, 0.09886771245286669, 1, 3, 1],
- [12, 24, 0.03515608866627348, 0.008300090752201086, 0.04345617941847457, 1, 2, 0],
- [12, 25, 0.02112831751687818, 0.07223272662848533, 0.09336104414536352, 1, 3, 1],
- [12, 26, 0.1775091239215047, 0.1611450236151337, 0.3386541475366385, 1, 1, 1],
- [12, 28, 0.01239927190285539, 0.010630447602192, 0.02302971950504739, 1, 2, 0],
- [12, 29, 0.01305671059301914, 0.009969589662362952, 0.0230263002553821, 1, 2, 0],
- [12, 30, 0.006106520807643618, 0.01501964804331584, 0.02112616885095946, 1, 2, 0],
- [14, 15, 0.1240062700965975, 0.07055023087280403, 0.1945565009694015, 2, 3, 2],
- [14, 16, 0.04968169518424277, 0.04322317133962539, 0.09290486652386816, 2, 4, 2],
- [14, 17, 0.03301523267075585, 0.006938602753590835, 0.03995383542434668, 2, 2, 1],
- [14, 18, 0.02006635669718209, 0.0042781821914317, 0.02434453888861379, 2, 2, 0],
- [14, 20, 0.02233301521846701, 0.003089474062639977, 0.02542248928110699, 2, 3, 0],
- [14, 21, 0.03948359355880873, 0.03409086082661509, 0.07357445438542382, 2, 5, 2],
- [14, 22, 0.0268688773450427, 0.0214401774126719, 0.0483090547577146, 2, 5, 2],
- [14, 23, 0.01484527139830796, 0.004437309946058014, 0.01928258134436597, 2, 3, 0],
- [14, 24, 0.03462721449579641, 0.003757871643734362, 0.03838508613953077, 2, 2, 0],
- [14, 25, 0.06357218444057811, 0.1549937645200927, 0.2185659489606708, 2, 3, 2],
- [14, 26, 0.01465463614671243, 0.003872792297083958, 0.01852742844379638, 2, 1, 0],
- [14, 28, 0.03514614576841267, 0.01055993418218698, 0.04570607995059965, 2, 2, 1],
- [14, 29, 0.03706388753758103, 0.00812869954206062, 0.04519258707964165, 2, 2, 1],
- [14, 30, 0.2282750950032041, 0.2310589775978077, 0.4593340726010118, 2, 2, 2],
- [15, 16, 0.01428121180297797, 0.03049560777140135, 0.04477681957437932, 3, 4, 2],
- [15, 17, 0.2365900473291059, 0.06430920229086168, 0.3008992496199676, 3, 2, 2],
- [15, 18, 0.01866802394433401, 0.003914994869448416, 0.02258301881378243, 3, 2, 0],
- [15, 20, 0.02356819283235103, 0.005400571337284119, 0.02896876416963515, 3, 3, 1],
- [15, 21, 0.1063655984295545, 0.1098520926697359, 0.2162176910992904, 3, 5, 3],
- [15, 22, 0.113078754604692, 0.1193807004556669, 0.2324594550603589, 3, 5, 3],
- [15, 23, 0.01760198994331581, 0.004394350408904264, 0.02199634035222007, 3, 3, 1],
- [15, 24, 0.0255055798649768, 0.003455505302173749, 0.02896108516715055, 3, 2, 0],
- [15, 25, 0.02286215331427334, 0.05572789891617332, 0.07859005223044666, 3, 3, 2],
- [15, 26, 0.01144159443320607, 0.005868313383528745, 0.01730990781673482, 3, 1, 0],
- [15, 28, 0.01363916550740871, 0.01152910521301816, 0.02516827072042686, 3, 2, 1],
- [15, 29, 0.01851254280568752, 0.01005463911380465, 0.02856718191949216, 3, 2, 1],
- [15, 30, 0.07122084719427205, 0.1468009520008997, 0.2180217991951718, 3, 2, 2],
- [16, 17, 0.01782636504763381, 0.004049733645987459, 0.02187609869362126, 4, 2, 1],
- [16, 18, 0.02901428767197188, 0.007979068596454607, 0.03699335626842649, 4, 2, 1],
- [16, 20, 0.02145658661219722, 0.004828023565954753, 0.02628461017815198, 4, 3, 1],
- [16, 21, 0.04160074147630265, 0.0207606784884952, 0.06236141996479785, 4, 5, 3],
- [16, 22, 0.05146197934676123, 0.01823400830047511, 0.06969598764723633, 4, 5, 3],
- [16, 23, 0.01822949401965692, 0.003315249491921823, 0.02154474351157875, 4, 3, 1],
- [16, 24, 0.03676885352758808, 0.006253436543370671, 0.04302229007095875, 4, 2, 1],
- [16, 25, 0.1841429087738894, 0.3152593422346555, 0.4994022510085449, 4, 3, 3],
- [16, 26, 0.03417832955442882, 0.01682864955963237, 0.05100697911406119, 4, 1, 1],
- [16, 28, 0.09860322016656659, 0.04068814080185486, 0.1392913609684215, 4, 2, 2],
- [16, 29, 0.1080970519952679, 0.03688377612775603, 0.144980828123024, 4, 2, 2],
- [16, 30, 0.0377960989989632, 0.06418358230375337, 0.1019796813027166, 4, 2, 2],
- [17, 18, 0.01185456228440142, 0.007796983061071273, 0.01965154534547269, 2, 2, 0],
- [17, 20, 0.0332281399389085, 0.01516984390639092, 0.04839798384529942, 2, 3, 1],
- [17, 21, 0.03131317673510807, 0.04980166629871462, 0.08111484303382269, 2, 5, 2],
- [17, 22, 0.02658918454287775, 0.05018726477890903, 0.07677644932178679, 2, 5, 2],
- [17, 23, 0.02475247746828598, 0.0169563833600419, 0.04170886082832788, 2, 3, 1],
- [17, 24, 0.02250824430772414, 0.006885755628265392, 0.02939399993598953, 2, 2, 0],
- [17, 25, 0.008406025942038792, 0.03106161612057492, 0.03946764206261372, 2, 3, 1],
- [17, 26, 0.009282829245117721, 0.01432266485153354, 0.02360549409665125, 2, 1, 0],
- [17, 28, 0.02505746434873073, 0.02439269819223868, 0.04945016254096941, 2, 2, 1],
- [17, 29, 0.02334545268294474, 0.02603360928442499, 0.04937906196736973, 2, 2, 1],
- [17, 30, 0.006120114170392863, 0.04613425130634214, 0.052254365476735, 2, 2, 1],
- [18, 20, 0.02835867055729394, 0.03051095907045615, 0.05886962962775009, 2, 3, 1],
- [18, 21, 0.006524067143595717, 0.02097381073320005, 0.02749787787679577, 2, 5, 1],
- [18, 22, 0.005951114890757478, 0.01734555223255374, 0.02329666712331122, 2, 5, 1],
- [18, 23, 0.02679758037211821, 0.02171809821499259, 0.0485156785871108, 2, 3, 1],
- [18, 24, 0.02794861768861829, 0.01091010179620578, 0.03885871948482407, 2, 2, 0],
- [18, 25, 0.00547466390308578, 0.05096953940013922, 0.056444203303225, 2, 3, 1],
- [18, 26, 0.04713529782381884, 0.147517174759375, 0.1946524725831938, 2, 1, 1],
- [18, 28, 0.005834608457505859, 0.0152237752272461, 0.02105838368475195, 2, 2, 0],
- [18, 29, 0.009809673821294161, 0.01961999091486498, 0.02942966473615914, 2, 2, 0],
- [18, 30, 0.004106924911106094, 0.0212640024303487, 0.02537092734145479, 2, 2, 0],
- [20, 21, 0.0106282403425438, 0.04039821513711003, 0.05102645547965383, 3, 5, 2],
- [20, 22, 0.01018346538718277, 0.03712847397201344, 0.0473119393591962, 3, 5, 2],
- [20, 23, 0.08066982082609707, 0.09697970751966636, 0.1776495283457634, 3, 3, 2],
- [20, 24, 0.0235382382132855, 0.01604967777748543, 0.03958791599077093, 3, 2, 0],
- [20, 25, 0.003423699228229319, 0.03729116441894532, 0.04071486364717464, 3, 3, 1],
- [20, 26, 0.03010903973132922, 0.0792493655437253, 0.1093584052750545, 3, 1, 1],
- [20, 28, 0.006896520869508807, 0.01763535757626972, 0.02453187844577853, 3, 2, 0],
- [20, 29, 0.008452797226508749, 0.01635647793775643, 0.02480927516426518, 3, 2, 0],
- [20, 30, 0.003095558108305428, 0.02500421480139507, 0.0280997729097005, 3, 2, 0],
- [21, 22, 0.1252684968513963, 0.136515693167626, 0.2617841900190223, 5, 5, 4],
- [21, 23, 0.03150028194750475, 0.01038169657309909, 0.04188197852060385, 5, 3, 2],
- [21, 24, 0.0291189462349777, 0.004949542712431419, 0.03406848894740912, 5, 2, 0],
- [21, 25, 0.05817486040851345, 0.2337789498314103, 0.2919538102399237, 5, 3, 3],
- [21, 26, 0.02161672916870432, 0.01542046740137113, 0.03703719657007545, 5, 1, 1],
- [21, 28, 0.008853112135224245, 0.01473257967171467, 0.02358569180693892, 5, 2, 1],
- [21, 29, 0.01104149126852355, 0.0112121954071869, 0.02225368667571045, 5, 2, 1],
- [21, 30, 0.01981188214469076, 0.04607061916870642, 0.06588250131339718, 5, 2, 2],
- [22, 23, 0.2417023075963993, 0.09748281763954433, 0.3391851252359436, 5, 3, 3],
- [22, 24, 0.02866820036560731, 0.004389002955129634, 0.03305720332073694, 5, 2, 1],
- [22, 25, 0.05951378230290671, 0.2182001187994253, 0.277713901102332, 5, 3, 3],
- [22, 26, 0.0216180875663217, 0.01912704074549006, 0.04074512831181176, 5, 1, 1],
- [22, 28, 0.01017154387527456, 0.006751614251023627, 0.01692315812629819, 5, 2, 1],
- [22, 29, 0.008484165669395357, 0.006352798226140098, 0.01483696389553545, 5, 2, 1],
- [22, 30, 0.01671073245892866, 0.04349804879476411, 0.06020878125369277, 5, 2, 2],
- [23, 24, 0.04562441011343223, 0.02002989348257047, 0.0656543035960027, 3, 2, 1],
- [23, 25, 0.002681149687355626, 0.02379196502622149, 0.02647311471357712, 3, 3, 1],
- [23, 26, 0.02520734946693424, 0.08017222321450257, 0.1053795726814368, 3, 1, 1],
- [23, 28, 0.006108324165705776, 0.01315945866988892, 0.0192677828355947, 3, 2, 0],
- [23, 29, 0.007832385982193907, 0.01244156292841715, 0.02027394891061106, 3, 2, 0],
- [23, 30, 0.002148132526385406, 0.0162182445937851, 0.0183663771201705, 3, 2, 0],
- [24, 25, 0.003280169877064053, 0.04232444793320719, 0.04560461781027124, 2, 3, 0],
- [24, 26, 0.005616845573718578, 0.03457432648711956, 0.04019117206083814, 2, 1, 0],
- [24, 28, 0.01662564599904145, 0.08682615622766726, 0.1034518022267087, 2, 2, 1],
- [24, 29, 0.02380609019454122, 0.08066548140193953, 0.1044715715964808, 2, 2, 1],
- [24, 30, 0.001779848103066491, 0.03558210318886525, 0.03736195129193174, 2, 2, 0],
- [25, 26, 0.06593316758122636, 0.02166592663716863, 0.08759909421839499, 3, 1, 1],
- [25, 28, 0.02889704020936961, 0.005342768040509653, 0.03423980824987927, 3, 2, 1],
- [25, 29, 0.02814406496232846, 0.01687874749838335, 0.04502281246071182, 3, 2, 1],
- [25, 30, 0.1123773177282409, 0.107330048901509, 0.2197073666297499, 3, 2, 2],
- [26, 28, 0.01202310187965289, 0.0100752849569055, 0.0220983868365584, 1, 2, 0],
- [26, 29, 0.01098659894875614, 0.0106778458846393, 0.02166444483339544, 1, 2, 0],
- [26, 30, 0.008888531742284057, 0.0220072024775357, 0.03089573421981976, 1, 2, 0],
- [28, 29, 0.3253931306175987, 0.3786081317863912, 0.70400126240399, 2, 2, 2],
- [28, 30, 0.007946759742122602, 0.03360599467213372, 0.04155275441425633, 2, 2, 1],
- [29, 30, 0.01669873349292508, 0.03504162520377113, 0.05174035869669621, 2, 2, 1]
+[2, 3, 0.02851572177464722, 0.01992394838090668, 0.04843967015555389, 4, 3, 1],
+ [2, 4, 0.2913031811286725, 0.1581095173619919, 0.4494126984906644, 4, 2, 2],
+ [2, 5, 0.04313828130286183, 0.09337388689236253, 0.1365121681952244, 4, 3, 2],
+ [2, 6, 0.05037434713194238, 0.07113225549859428, 0.1215066026305367, 4, 6, 3],
+ [2, 7, 0.2804886800096655, 0.2001828066808252, 0.4806714866904907, 4, 4, 3],
+ [2, 8, 0.07183821900324161, 0.1469389589305462, 0.2187771779337878, 4, 5, 3],
+ [2, 9, 0.03082407077478325, 0.09900473652454521, 0.1298288072993285, 4, 3, 2],
+ [2, 10, 0.02245776059232202, 0.02955557233236829, 0.05201333292469031, 4, 3, 1],
+ [3, 4, 0.03717045364745913, 0.02520976460488304, 0.06238021825234218, 3, 2, 0],
+ [3, 5, 0.02873335174526813, 0.03479214292405394, 0.06352549466932207, 3, 3, 1],
+ [3, 6, 0.1236923855363388, 0.2512471049857198, 0.3749394905220587, 3, 6, 3],
+ [3, 7, 0.01909635400892135, 0.02551889926711521, 0.04461525327603656, 3, 4, 1],
+ [3, 8, 0.02488014112561441, 0.05406148356625361, 0.07894162469186802, 3, 5, 2],
+ [3, 9, 0.08440837590482446, 0.2181470609147132, 0.3025554368195377, 3, 3, 2],
+ [3, 10, 0.1267967238159999, 0.1611592144212058, 0.2879559382372058, 3, 3, 2],
+ [4, 5, 0.03705892982325252, 0.07620033982326219, 0.1132592696465147, 2, 3, 1],
+ [4, 6, 0.01210885428759886, 0.04049276326654051, 0.05260161755413936, 2, 6, 1],
+ [4, 7, 0.03773982374178716, 0.04469577929352821, 0.08243560303531537, 2, 4, 1],
+ [4, 8, 0.02406357502679824, 0.04542327412998536, 0.06948684915678359, 2, 5, 1],
+ [4, 9, 0.04518375503528457, 0.08175199548949739, 0.126935750524782, 2, 3, 1],
+ [4, 10, 0.05271458150974553, 0.07030981080391227, 0.1230243923136578, 2, 3, 1],
+ [5, 6, 0.1359282078272841, 0.1540926795656895, 0.2900208873929736, 3, 6, 3],
+ [5, 7, 0.09099743539437326, 0.04199316180345154, 0.1329905971978248, 3, 4, 2],
+ [5, 8, 0.1895195673806065, 0.2930011407919719, 0.4825207081725784, 3, 5, 3],
+ [5, 9, 0.1148199627842869, 0.1105571269028783, 0.2253770896871652, 3, 3, 2],
+ [5, 10, 0.1270434887308012, 0.1100230063742557, 0.2370664951050569, 3, 3, 2],
+ [6, 7, 0.09069770755435493, 0.0484084497358865, 0.1391061572902414, 6, 4, 3],
+ [6, 8, 0.1325890592140632, 0.1385237411340729, 0.2711128003481361, 6, 5, 4],
+ [6, 9, 0.1237432424538594, 0.1610336810828299, 0.2847769235366894, 6, 3, 3],
+ [6, 10, 0.2074649804257667, 0.132053108013182, 0.3395180884389487, 6, 3, 3],
+ [7, 8, 0.0894441901425615, 0.1431622704391284, 0.2326064605816899, 4, 5, 3],
+ [7, 9, 0.06037024754303832, 0.114173814968622, 0.1745440625116604, 4, 3, 2],
+ [7, 10, 0.02455907863678367, 0.02700169365828593, 0.0515607722950696, 4, 3, 1],
+ [8, 9, 0.2356164682007381, 0.275411073609017, 0.5110275418097552, 5, 3, 3],
+ [8, 10, 0.05927356969559661, 0.02598780235339034, 0.08526137204898694, 5, 3, 2],
+ [9, 10, 0.1776480482199785, 0.09671451255218226, 0.2743625607721607, 3, 3, 2]
],
"headers": [
["Site 1", "Index of site 1"],
@@ -300,56 +60,56 @@
"branch attributes":{
"0":{
"Baboon":{
- "models.DNA.GTR.ModelDescription":0
+ "models.codon.MG_REV.ModelDescription":0
},
"Cat":{
- "models.DNA.GTR.ModelDescription":0.7933191636859576
+ "models.codon.MG_REV.ModelDescription":0.8288168941011919
},
"Chimp":{
- "models.DNA.GTR.ModelDescription":0
+ "models.codon.MG_REV.ModelDescription":0
},
"Cow":{
- "models.DNA.GTR.ModelDescription":0.8094119333244753
+ "models.codon.MG_REV.ModelDescription":0.8164924147537205
},
"Horse":{
- "models.DNA.GTR.ModelDescription":0.2769077630163064
+ "models.codon.MG_REV.ModelDescription":0.2841592907567805
},
"Human":{
- "models.DNA.GTR.ModelDescription":0
+ "models.codon.MG_REV.ModelDescription":0
},
"Mouse":{
- "models.DNA.GTR.ModelDescription":0.1094921058577506
+ "models.codon.MG_REV.ModelDescription":0.1035113121392619
},
"Node1":{
- "models.DNA.GTR.ModelDescription":0.4820782253393885
+ "models.codon.MG_REV.ModelDescription":0.5236339695213962
},
"Node12":{
- "models.DNA.GTR.ModelDescription":0
+ "models.codon.MG_REV.ModelDescription":0
},
"Node2":{
- "models.DNA.GTR.ModelDescription":0.08259105925424247
+ "models.codon.MG_REV.ModelDescription":0.08766202644314423
},
"Node3":{
- "models.DNA.GTR.ModelDescription":0.2526911684326281
+ "models.codon.MG_REV.ModelDescription":0.2629569437833751
},
"Node8":{
- "models.DNA.GTR.ModelDescription":0.06531857233184223
+ "models.codon.MG_REV.ModelDescription":0.07018254851044582
},
"Node9":{
- "models.DNA.GTR.ModelDescription":0.03361817454867485
+ "models.codon.MG_REV.ModelDescription":0.03334231749233734
},
"Pig":{
- "models.DNA.GTR.ModelDescription":0
+ "models.codon.MG_REV.ModelDescription":0
},
"Rat":{
- "models.DNA.GTR.ModelDescription":0.0888784436278628
+ "models.codon.MG_REV.ModelDescription":0.1018034850081214
},
"RhMonkey":{
- "models.DNA.GTR.ModelDescription":0
+ "models.codon.MG_REV.ModelDescription":0
}
},
"attributes":{
- "models.DNA.GTR.ModelDescription":{
+ "models.codon.MG_REV.ModelDescription":{
"attribute type":"branch length",
"display order":0
}
@@ -358,32 +118,32 @@
"data partitions":{
"0":{
"coverage": [
-[0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]
+[0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
],
"name":"bgm.filter.default"
}
},
"fits":{
- "models.DNA.GTR.ModelDescription":{
- "AIC-c":472.7691802214979,
- "Log Likelihood":-210.2027719289308,
+ "models.codon.MG_REV.ModelDescription":{
+ "AIC-c":508.3788244913426,
+ "Log Likelihood":-208.6011769515537,
"Rate Distributions":null,
"display order":0,
- "estimated parameters":24
+ "estimated parameters":31
}
},
"input":{
- "datatype":"nucleotide",
- "file name":"/tmp/tmpSz4m4X/job_working_directory/000/3/working/bgm_input.fa",
+ "datatype":"codon",
+ "file name":"/tmp/tmp_Fhyr9/job_working_directory/000/3/working/./bgm_input.fa",
"number of sequences":10,
- "number of sites":30,
+ "number of sites":10,
"trees":{
"0":"((((Pig:0.147969,Cow:0.21343)Node3:0.08509899999999999,Horse:0.165787,Cat:0.264806)Node2:0.058611,((RhMonkey:0.002015,Baboon:0.003108)Node9:0.022733,(Human:0.004349,Chimp:0.000799)Node12:0.011873)Node8:0.101856)Node1:0.340802,Rat:0.050958,Mouse:0.09795)"
}
},
"settings":{
"burn-in":10000,
- "data-type":"nucleotide",
+ "data-type":"codon",
"max-parents":1,
"min-subs":1,
"samples":100,
@@ -394,15 +154,15 @@
"timers":{
"Baseline fit":{
"order":1,
- "timer":0
+ "timer":3
},
"Network inference":{
"order":2,
- "timer":1
+ "timer":0
},
"Overall":{
"order":0,
- "timer":1
+ "timer":3
}
}
}
\ No newline at end of file
diff -r 7b3f9c78cf6d -r d02c8e6f7f2a test-data/busted-out1.json
--- a/test-data/busted-out1.json Wed Aug 21 12:26:38 2019 -0400
+++ b/test-data/busted-out1.json Thu Feb 13 15:03:27 2020 -0500
@@ -1,361 +1,394 @@
{
- "analysis":{
- "info":"BUSTED (branch-site unrestricted statistical test of episodic diversification) uses a random effects branch-site model fitted jointly to all or a subset of tree branches in order to test for alignment-wide evidence of episodic diversifying selection. Assuming there is evidence of positive selection (i.e. there is an omega > 1), BUSTED will also perform a quick evidence-ratio style analysis to explore which individual sites may have been subject to selection.",
- "version":"1.2",
- "citation":"*Gene-wide identification of episodic selection*, Mol Biol Evol. 32(5):1365-71",
- "authors":"Sergei L Kosakovsky Pond",
- "contact":"spond@temple.edu",
- "requirements":"in-frame codon alignment and a phylogenetic tree (optionally annotated with {})"
+ "Evidence Ratios":{
+ "constrained": [
+[1.766356514902524, 0.9484374805763239, 0.9571091930814299, 1.845676838710576, 1.513819401189324, 2.11256226458989, 7.366103227625151, 3.937756516229049, 2.586067836907899, 0.722379841928909, 0.3151239046214458, 1.502917468627881, 0.6499879033472316, 1.047489715978757, 1.060206108705189, 0.5038296392390414, 0.8532658611088545, 1.114374823999701, 0.5611409841208096, 0.6702870396165613, 0.4604115167079821, 0.3988433224622866, 2.47019807349414, 0.9858342091732886, 1.106653406611749, 1.067348070135177, 1.77412165088655, 1.321424873505688, 1.90457149631063, 0.7888758683589224, 0.7229203540914775, 0.8813401886687667, 0.6954297746421804, 4.613654710605887, 0.4975309466317643, 1.84565076502724, 0.6214894235132998, 0.9480915704528677, 0.9669462933548731, 1.488081789562878, 1.368539685217942, 1.726522735566884, 1.222915324989829, 0.7085094082639855, 0.3168181005885327, 2.290014391709923, 0.6343005734674315, 0.8841633809961478, 1.508078414734822, 2.666352901083321, 1.732923983135172, 3.102011384229053, 1.585109653073893, 3.345181824497555, 7.193115253213268, 3.850321954428519, 3.233128500312913, 1.977820966308441, 2.047653340750355, 0.6643430465826362, 3.624272911205855, 1.67814994913239, 1.752817561416471, 3.277248182160172, 0.3406457937754578, 0.4841828665456315, 1.399775481724447, 0.5510187898414104, 0.6276769404480749, 0.4535822272441153, 0.4226923979745105, 2.950051361271033, 0.9999999999999982, 1.027733519332009, 2.963278030618241, 2.8935730521221, 1.881916301985038, 0.4490192221083247, 3.102588216900087, 0.7028469232610687, 2.792137897266834, 0.3889955246330017, 0.9360790804326219, 0.4572233386404743, 2.908919410553763, 0.8995968442944373, 0.3261344314757346, 1.080257865601265, 1.399763176607792, 1.534646955858424, 0.4277164444783946, 2.361993404905034, 2.175584822495568, 3.122529901767528, 0.4453847841440882, 1.711825080925545, 0.8458710509917922, 2.741896592382772, 0.576439632416141, 1.142294357680513, 0.8086330800808955, 2.943414796294152, 0.833291758377592, 1.615921141634484, 0.7252129604805458, 2.833655116179036, 0.9138779988368123, 0.6174720822006171, 1.834532902825704, 0.2316812685220093, 2.479235579982967, 0.4643862206171616, 6.530720225707355, 0.4975309466317643, 1.158125132567293, 0.2987944638927862, 3.78696693228073, 0.7343025200073082, 1.93339742618843, 0.3642707474760721, 1.028034824972818, 1.511057897004292, 0.2969890376651506, 0.987605711796378, 0.3709886418939366, 4.185741574214752, 3.002372601666337, 0.424383367760914, 0.4658081554322532, 0.4024556436060775, 2.540164510486854, 0.5199349857684811, 0.4626485320487528, 0.9349816613814522, 0.5525607476128181, 0.5855612460554309, 1.85872747574379, 1.064964125964651, 3.177687923317396, 2.593304657270028, 5.234187858164534, 2.966427299030309, 1.920561682721974, 2.245869881969924, 3.811870935099101, 2.099654636695842, 3.369504334172069, 0.6379165155453101, 3.119867019567397, 0.9211859677702382, 2.195241379859611, 1.767535349740496, 1.225677095999665, 1.347676192394215, 1.671173168407676, 1.179430472478473, 1.873629958128968, 1.972321068578892, 1.863249013159319, 1.501711930393218, 2.85458165498371, 0.5332817404709185, 0.7514817421990073, 0.2887801591578705, 1.93925520496415, 0.2163710715496819, 2.457406602553581, 0.4895227461773333, 2.731573653164397, 0.8923840424261161, 0.6288736610053396, 3.562511382204229, 0.8043427141817341, 2.97831687935463, 3.021636055180988, 1.919432168129229, 1.231674183402057, 3.382911261347008, 1.455440822286478, 1.714894279904311, 0.4763853457361669, 0.907985271671091, 0.9191891327337078, 0.8704988461364657, 0.4660185191281315, 0.6176233729242167, 0.9987767701341157]
+ ],
+ "optimized null": [
+[1.118923161648219, 0.9980202548897937, 0.9997654691276022, 1.028326548692021, 0.7919741374095479, 0.6742163346738066, 0.9701775068012184, 1.781350909123149, 2.014615609490285, 0.9375026657270238, 0.6503469909372603, 1.467509823797021, 1.009616470968526, 1.168421464905222, 0.59794016479865, 0.8088642155191522, 0.9570182332372693, 1.200458035608254, 0.9382406902547993, 0.971502044629861, 0.9494035585701087, 0.8642047320556682, 0.7618657208728498, 0.9877802717728724, 1.196913567892764, 1.219008654454505, 1.195602379971315, 1.386927451387816, 0.9612092240804505, 0.7608092856171619, 0.7774974434748834, 0.882472157999228, 1.287408843481257, 0.77835738564002, 0.9105718870056999, 0.9901735448217958, 0.7939955331410506, 1.000490010159418, 1.004589199921733, 1.297516080632708, 1.03030381955465, 0.8106679119008423, 1.81201409338234, 0.7198749295257847, 0.6994440009800842, 0.8437894137548632, 1.143486692785445, 0.9393973334278157, 0.8256667500261211, 0.7815159607314222, 0.5985208951864024, 0.8535790889335229, 1.025460140178824, 3.820941298927726, 1.291930691854327, 0.9067539623849099, 1.157350624394714, 0.998318955418969, 0.9161866303121252, 0.8876780413980894, 1.109157480575484, 1.092621268372832, 0.8972624848442422, 0.9889106716665784, 0.8341566095527148, 1.038544978108518, 1.714787775296502, 0.9137222760182561, 1.034926570525361, 0.8813745500117369, 0.8349529524516258, 1.213599287773434, 1, 1.089476250837934, 0.8899148576721072, 2.300141517859181, 0.6825541016975851, 1.003665786880968, 1.237110533718188, 1.020075909706045, 1.638150182736532, 0.9011618842606461, 0.9230020461155208, 0.751689080395277, 0.5897676439072257, 0.6404917862661024, 0.7469389376638015, 1.083533646483151, 0.7344437672842805, 1.131725226416453, 0.9190373093865288, 1.470665196381038, 1.267251236251085, 1.076738563303299, 0.9719321192139432, 1.046564634995135, 1.040861206200881, 1.432126587856311, 0.9607511063877517, 1.317983216727182, 1.009193498305615, 1.490294304430241, 0.9453834990966208, 0.9949520064421568, 0.9321847062820814, 1.012192223349541, 1.006095335695502, 1.015717182050207, 1.155947081675256, 0.7426317882836824, 0.8600656083242881, 0.8659102843696671, 2.043199066063688, 0.9105718870056999, 0.7755680708217269, 0.8691797858502243, 1.408772939677855, 0.9935920773928444, 0.776611704010421, 0.7417817446846022, 1.113087499879386, 1.540328788060018, 0.7887000169650941, 0.7125843942768558, 0.803768142354686, 1.030948607017191, 1.106410103708125, 0.8462900614413438, 0.9257201660506196, 0.9862223424699452, 2.874290057428853, 0.9765125041895547, 0.9522206558439166, 0.979008503258283, 0.8163413206500215, 0.7929865064112649, 1.054431661259741, 1.391867727782659, 1.55344883290767, 0.9159617667614252, 1.37597067666192, 1.180188215894089, 0.8980539087871242, 0.8445482715276972, 1.439858975048729, 0.8167533472760263, 1.611375099688448, 0.9949969190225336, 1.453373381083946, 0.8294327035809631, 1.883890801528407, 1.621067636191696, 0.7786019875784795, 1.241031199394852, 0.8699818919359624, 0.8969821406492622, 0.8552871694200248, 1.476143154036665, 0.7328425886346202, 1.12339872066542, 1.055700479953033, 0.8643592588676906, 0.8828252272762036, 0.8310350398630689, 1.509625875333898, 0.8258835645292275, 1.192338427340326, 0.988317199275236, 0.7869748564877793, 1.092663634718098, 1.540873058588039, 1.27733975846824, 1.071338379207414, 1.598643725487392, 2.039697563641063, 1.125982095744282, 0.8865373778453701, 0.896677110067575, 1.480314453817297, 0.6279749170263321, 0.9454481522954102, 0.8270407761576262, 0.924976567928722, 0.9460839037512674, 1.00781396274934, 1.11935672287797, 1.612656256447746]
+ ]
},
- "input":{
- "file name":"/Users/stephenshank/Documents/Galaxy/tools-iuc/tools/hyphy/test-data/absrel-in1.fa",
- "number of sequences":10,
- "number of sites":187,
- "partition count":1,
- "trees":{
- "0":"((((Pig:0.147969,Cow:0.21343)Node3:0.085099,Horse:0.165787,Cat:0.264806)Node2:0.058611,((RhMonkey:0.002015,Baboon:0.003108)Node9:0.022733,(Human:0.004349,Chimp:0.000799)Node12:0.011873)Node8:0.101856)Node1:0.340802,Rat:0.050958,Mouse:0.09795)"
- }
+ "Site Log Likelihood":{
+ "constrained": [
+[-10.45729861177352, -3.484017570185021, -3.811593093827024, -18.53808870245015, -17.92309552060635, -29.83947832086448, -32.51456888432799, -26.14022567456645, -18.98957484098232, -10.33347856776535, -16.45292539731993, -23.86010381033633, -20.00687543711394, -16.65179796964098, -21.99232160499268, -12.26652073720412, -10.69225356932102, -15.60314346893525, -11.01132866125176, -8.521297155687831, -8.203139397826641, -11.43545706508415, -24.90046120971902, -13.6386798900763, -14.85763270108216, -14.7030317250254, -22.05138318385674, -15.98662844335023, -21.8003647511144, -18.57068156644835, -22.299055200187, -14.20074227547402, -10.45246619974257, -29.65657150543187, -5.937537382195638, -33.78920222670538, -15.44637827577353, -4.279026884494699, -4.808492102928678, -24.63079311886252, -19.95624962482634, -20.75045752192579, -12.74902310767432, -18.99427847476613, -14.28731466672857, -24.54528292419485, -16.76361995667699, -15.30372003397147, -21.15548703165981, -23.72245288385755, -28.94171761244187, -31.14183824690388, -20.64762811392306, -24.08520562625058, -32.41122173355103, -27.15825647361205, -28.5179867447387, -21.82691317662457, -23.87561847496401, -15.96134254249656, -22.91741429446779, -22.8344267349475, -18.86994129807232, -24.15268806222941, -13.09988257350861, -6.987933615627104, -20.27062516100397, -11.6267899578313, -10.76199226925333, -9.365202828107813, -8.830802980942332, -22.25274148442388, -5.072420031658066, -11.5940578599292, -24.90254274563229, -26.4504338975355, -29.4914117779418, -14.39917492841001, -30.20915692724294, -15.07835940842867, -24.47922859714559, -9.963108156848188, -12.02484522350882, -10.47082266101894, -32.61997541577167, -22.41917549927993, -15.45008408736274, -18.58952738985428, -24.90070817016433, -16.46583864612196, -9.349881275491541, -21.92481437356786, -23.89225210843373, -25.41089239829785, -13.11222485538043, -23.55550258653596, -13.5386142710809, -25.36851139033049, -12.93730850270479, -18.80108927581331, -14.23685164495206, -22.26383266334966, -10.55622492327747, -21.48906087213606, -10.38853588609826, -24.53689740053753, -11.36767104821917, -6.908653364620656, -21.84280151068446, -17.93716231251139, -24.46209768558333, -8.752467536320703, -25.50970610456629, -5.937537382195638, -26.74893035287963, -11.9403240118369, -26.13347920733979, -8.842765208651075, -22.25304376265024, -12.64504365092861, -11.95155411820952, -16.44565617489921, -12.21136817821285, -19.4495506152908, -12.03636955134022, -26.76158975846396, -24.28299039768532, -10.41253856833306, -18.04928878164386, -12.66411737564947, -24.89370230796465, -13.28589560426102, -12.14998856202217, -15.22485748978356, -11.10445442252986, -15.26584291199847, -21.18251113737594, -17.4492424252813, -22.91858352137089, -32.12984803882419, -34.72655653940613, -29.46637589613799, -23.83622026476351, -25.19174747094332, -26.15371116437007, -28.38602800921473, -24.3904479288928, -11.83470465315949, -22.99304711962677, -14.1052741197831, -27.4333232450484, -16.96102482386623, -16.48031664612245, -16.51933846935232, -17.67884199792057, -14.76033658655028, -19.64011886967656, -21.73563121093473, -27.07964360348662, -23.31227029359847, -30.36351219328728, -14.39405059091475, -9.0012985358923, -13.02696101249317, -22.60078004596954, -16.83684027122174, -27.58316083045541, -5.435892920303646, -29.48238449481695, -10.75922123674425, -14.39572297485616, -21.65465418121673, -13.81883365226544, -26.28515446199947, -25.94713203139664, -30.32048162447653, -18.74338069598867, -29.89507747948719, -18.59896471825973, -26.6197512688528, -7.057151084653121, -20.11123180495239, -13.68737039495877, -13.8591446292234, -7.100328940735415, -7.27389954199287, -20.4341543043075]
+ ],
+ "optimized null": [
+[-10.000746412889, -3.534975268563031, -3.855196330132343, -17.9531754129423, -17.27523311609171, -28.69737251844359, -30.487403824811, -25.3469865397239, -18.73986474128691, -10.5941470716412, -17.17746554049388, -23.83626257910331, -20.44724749063709, -16.76105507711494, -21.41959368469256, -12.7399136042534, -10.80700483642069, -15.67755309754298, -11.52536299421752, -8.892434491135736, -8.926852661062641, -12.20869809997624, -23.72417791244537, -13.64065197048924, -14.93603840556554, -14.8358925422005, -21.65672787001029, -16.03500867314082, -21.11654452541332, -18.53445530201509, -22.37183650032519, -14.20202582413271, -11.06832299336804, -27.87698168792971, -6.541952472626266, -33.16649523981481, -15.69133721810966, -4.332820962725578, -4.846683129097396, -24.49375694739045, -19.67235910587276, -19.99445132707328, -13.14222447425636, -19.010192624522, -15.07927260784268, -23.54687249677092, -17.35293440007094, -15.36431670327766, -20.55308672706422, -22.49522159373395, -27.87861362498808, -29.85147043539681, -20.21211595634147, -24.21818138264384, -30.69423513967148, -25.71221557332896, -27.49066994877449, -21.14323500088168, -23.07138885914685, -16.25115300126723, -21.73336130310753, -22.40531441170235, -18.20030993527343, -22.95453268750557, -13.99546052997636, -7.751046909853225, -20.47360263421817, -12.13254771763505, -11.26205241801605, -10.02950893550899, -9.511533636871842, -21.36450946580444, -5.072420031658067, -11.65239902588355, -23.69961716091314, -26.2209124593937, -28.47720772549854, -15.20352359389407, -29.28969870111495, -15.45085261296868, -23.94598869120682, -10.80322523133013, -12.0107767142687, -10.96797346503774, -31.02416709659281, -22.07946508441355, -16.27875786287543, -18.59255520779903, -24.25576326194178, -16.16128150518837, -10.11474753171002, -21.45102326094385, -23.35180477003816, -24.34618548249837, -13.89257222918985, -23.06345551040454, -13.74605107743702, -24.71902198635289, -13.44815326344599, -18.94415314361011, -14.45841315258903, -21.58323588087952, -10.68243175660201, -21.00409493400298, -10.63960151353855, -23.50744845859135, -11.46380607942174, -7.40636973341585, -21.38093160255466, -19.10200007557443, -23.40340080290285, -9.37553226377444, -24.34770562165953, -6.541952472626266, -26.34796839682552, -13.00811807862387, -25.1446328603122, -9.145170849858582, -21.34095019187551, -13.35620130330373, -12.03104276076478, -16.46484206770943, -13.18805899222384, -19.12316542756082, -12.80950895147612, -25.36038522816893, -23.28470818774974, -11.10276351543467, -18.73608690839096, -13.56041431572836, -25.01727916833232, -13.9161793832148, -12.87181769553462, -15.27087090233286, -11.49472359736922, -15.56907833534053, -20.61562094868151, -17.71694784548008, -22.20290716981454, -31.08913439244855, -33.39050427276854, -28.54469152779638, -23.07607739799698, -24.21370116505611, -25.18013621147851, -27.44183700650422, -23.65277019084076, -12.27923687244804, -22.22914406475213, -14.0003541619513, -27.28037045002411, -16.87452367228698, -16.02656793234758, -16.4368993455096, -17.02603324065743, -14.48658558781633, -18.85592317056478, -21.445852863631, -26.14649750870843, -23.02202321164394, -29.3687914002132, -14.87698920390545, -9.162378872547357, -14.08396726867812, -22.35033791702401, -18.17629921418486, -26.85997070710383, -6.138465689345856, -28.23794764233195, -10.96169835180006, -15.29189705116706, -20.62896804216628, -14.10547218000938, -25.66295172482926, -25.55413515032033, -29.78710785677539, -18.41457433641119, -28.56728137258359, -18.61591042688218, -25.61514478015318, -7.742583058377544, -20.01785764703301, -13.69364689624316, -13.94240945383619, -7.871642437614435, -7.868530143948813, -20.91326095114609]
+ ],
+ "unconstrained": [
+[-9.888379652897939, -3.536956975958899, -3.855430888511407, -17.92524264198113, -17.50845965857853, -29.09157676668757, -30.51768005233528, -24.76961452555787, -18.03943632860708, -10.65868274934065, -17.60771476681289, -23.45269561216572, -20.4376769636146, -16.6054014145564, -21.93385827359542, -12.9520378226385, -10.85093767163684, -15.49484991723633, -11.58911175769067, -8.921346396691311, -8.978773985704009, -12.35464367982677, -23.99616287059628, -13.65294697344841, -14.75629218887099, -14.63785459209203, -21.4780777279763, -15.70791783931325, -21.15610770415758, -18.80782786477065, -22.62351142339454, -14.32705386381445, -10.81569144349841, -28.12755118363321, -6.63563490222878, -33.17637029323138, -15.92201466162742, -4.332331072581934, -4.842104427446767, -24.23330521785812, -19.64250537668504, -20.20434811557675, -12.547785488861, -19.33887041557516, -15.4367421517065, -23.71672482205896, -17.21885230292473, -15.42683344726171, -20.74465076426493, -22.74174129986231, -28.39190746698947, -30.00978751219203, -20.18697452723667, -22.87768457704827, -30.43809737982556, -25.8100997042818, -27.34453650032288, -21.14491746000365, -23.1589240493258, -16.37029916899328, -21.62976060249833, -22.31673476907595, -18.30871676975877, -22.9656839608183, -14.17679464299017, -7.713226235808525, -19.93431330744026, -12.22277632689638, -11.22772194016784, -10.15578153700462, -9.691913536959838, -21.17091890362336, -5.072420031658067, -11.56670194893985, -23.81624664728228, -25.38794180884747, -28.85912121067668, -15.19986450963457, -29.07692025541677, -15.43097556716119, -23.45242102332656, -10.90729559707754, -12.09090054194056, -11.25340596248809, -31.55219374013023, -22.52498406608164, -16.57052970348788, -18.51232761277223, -24.56440510741808, -16.03753828771942, -10.19917609135148, -21.06530844796211, -23.11495459612987, -24.27224885909952, -13.92104154234985, -23.01794248639294, -13.70600262406975, -24.35986152238043, -13.48819316139627, -18.66805044150527, -14.4492616572491, -21.18426226067477, -10.73859637126286, -21.00915571172136, -10.7098258147646, -23.49532996174187, -11.45772924514136, -7.390774787133855, -21.23601161044981, -19.39955500699172, -23.5541474067981, -9.519506237286315, -23.6331888724584, -6.63563490222878, -26.60212792035497, -13.14832336553394, -24.80191379036194, -9.151599391331736, -21.5937649828387, -13.65490152701742, -11.92390507531763, -16.03284617533124, -13.42542822929183, -19.46202235330671, -13.02795338302471, -25.32990587208053, -23.18358755436579, -11.26965663135059, -18.81327019488709, -13.57428776606662, -23.96147346112334, -13.93994710685256, -12.92077618523389, -15.29208585316513, -11.69764632373376, -15.80102740870741, -20.56261903661609, -17.38630131122748, -21.76242965716022, -31.17691504697109, -33.07134484404992, -28.37901759704339, -23.18360257842184, -24.38265454953325, -24.81559103668038, -27.64425513672643, -23.17568227719417, -12.28425251073614, -21.85525674064724, -14.18736746348983, -26.64703123652192, -16.39143870542445, -16.27682322339721, -16.22095669907547, -17.16531612207426, -14.59530491502789, -19.01224116633539, -21.05642015432602, -26.45732185834116, -22.90566454933433, -29.31458689156966, -15.02275599163344, -9.287006901120908, -14.26905058779356, -21.93847606157545, -18.36760069262192, -26.6840542632031, -6.150217270208246, -28.47750662196133, -10.87307993496604, -14.85954787421955, -20.38418844062237, -14.03656349147213, -25.19379612663061, -24.84133360657191, -29.66845222794427, -18.53500632737776, -28.67634082079026, -18.22365589287899, -26.08039983450566, -7.798679287046689, -20.20775892609134, -13.77163377000268, -13.9978334745163, -7.863858845763236, -7.755775978219822, -20.4353782829297]
+ ]
+ },
+ "Synonymous site-posteriors": [
+[0.08576487129701713, 0.2936722378990316, 0.2901632602723997, 0.01635516164580625, 0.0171445713661009, 0.000329807826277061, 2.384037236058195e-06, 0.003474937198538037, 0.1657001102485818, 0.4931122461392571, 0.6116781976326224, 0.1232572132258079, 0.3167287850643093, 0.3360418775747802, 0.09625774163526932, 0.7077210076579118, 0.8230716605433912, 0.4692840075680767, 0.8542599193835906, 0.8678806224860721, 0.7187694305926973, 0.8652759434333591, 0.006733209198735493, 0.5563418685268529, 0.548770039188077, 0.1117221464925625, 0.06375767530950946, 0.2544248885020188, 0.01241307080226442, 0.06415938924723534, 0.0664819611257975, 0.5678603832955883, 0.5701480360753304, 0.01716185680432071, 0.7450690448837864, 4.340363369344909e-06, 0.1054553312659123, 0.2962973099054295, 0.2887729969101556, 0.002139003370945352, 0.009013172357941268, 0.1358034694997206, 0.4571022356539327, 0.03050258030555141, 0.6104018187033817, 0.0009310184681936825, 0.05125568890333056, 0.2012729288816644, 0.02168623857883216, 0.005190644975220393, 0.0003844182663365903, 2.025101452550204e-05, 0.2653166678500586, 0.002736950624682267, 4.330160538654619e-05, 0.002447017669235062, 1.04185776899838e-05, 0.07686655084745994, 0.04255051609568109, 0.07964927182431392, 0.009868735494425898, 0.003987427214854124, 0.1864468621560382, 0.02614830208528422, 0.339871175815004, 0.9584270556742166, 0.1208451401789099, 0.8379535111570964, 0.4399112612280809, 0.6546600093353926, 0.6014957564153406, 0.03692874096493579, 0.2645541257391173, 0.877048492043487, 0.005212760236057918, 0.02626182426280086, 0.0003466347596566336, 0.2143323363123782, 3.94830951316172e-06, 0.4695770030113981, 0.141253166719253, 0.287277996900563, 0.529618089155993, 0.7751260138271018, 1.589794382004903e-06, 0.01061110460382564, 0.06904202423665572, 0.1222752760738798, 0.009436108368219053, 0.1756755023547773, 0.8674741705013883, 0.006953150480735887, 0.01485544007614186, 0.01061671400804696, 0.4622922362107368, 0.006976448397641074, 0.2288428608566239, 0.04492921236889752, 0.4792814192644717, 0.08021780746327278, 0.4272287756026639, 0.04187262145239815, 0.7448375318386113, 0.1041516052437809, 0.7758641911259492, 0.04153272254198651, 0.8730527081784645, 0.9061533002525032, 0.007394637725624075, 0.3286876779500328, 0.003007591552118394, 0.7696698519008212, 0.01472154002347215, 0.7450690448837864, 0.0002833970218347724, 0.4752847620805873, 0.06772419306275075, 0.7916442061973822, 0.04768815546756307, 0.633646799271313, 0.8506170933861232, 0.5333086229236574, 0.4601664067609844, 0.1298585434125494, 0.5258807564626594, 0.004910934759931754, 0.005326392789739794, 0.8568922356649976, 0.1781177185740091, 0.2618990376844352, 0.02043267281856545, 0.1513767944689721, 0.390161257271147, 0.2016761548930196, 0.862737391517766, 0.08518368394903716, 0.08643358463113204, 0.05626956022636653, 0.01204362533281676, 0.0001127787870965998, 9.187529415014566e-05, 0.0291337834475492, 0.00445510836740222, 0.000433375749053344, 0.01045459853680832, 0.02886192573391665, 0.01378875281992316, 0.419096617458437, 0.08903224698878176, 0.6525609111129962, 0.000772784141393912, 0.1484449334606463, 0.3645995750997711, 0.1075676751865187, 0.05248459777601974, 0.760566182374103, 0.09207060671403174, 0.05268528446916099, 0.0009595976424648991, 0.01801675181476272, 0.0003997370600438763, 0.4402401340454297, 0.7531135804916973, 0.4676233954749258, 0.006368990121970666, 0.1181278057317597, 0.0001342462574260838, 0.9089018067832817, 0.0004345263536072176, 0.8867574663987829, 0.3111239693194546, 0.02252285354211625, 0.2512560362419685, 0.02269736493711449, 0.006974745835283193, 0.001246559659240012, 0.1018711078071347, 0.001887551089155725, 0.1122951541441214, 0.003158025675593529, 0.9204927908967985, 0.262934005368038, 0.5690451557167514, 0.2158987219764257, 0.9551133675001365, 0.9600236276711078, 0.02872243122605889],
+ [0.6588352549067005, 0.6300104042707274, 0.6308571396167474, 0.7628498871463081, 0.8812042447619804, 0.6450891271407698, 0.05702739009473294, 0.9052573432113765, 0.8322529842816521, 0.50204312688312, 0.3866851002627893, 0.8747673220745895, 0.6811185218928401, 0.6610720252813483, 0.8929509703524842, 0.2915251071042961, 0.176811569233057, 0.5263591043980159, 0.1456890777980846, 0.1319463960095295, 0.2805572096643838, 0.1345797208549885, 0.9194135193694579, 0.4431254580098209, 0.4501541421700466, 0.8327692240155901, 0.9249414026465288, 0.7390951865327187, 0.8744353425012321, 0.9003053400605937, 0.8607595493014167, 0.4302521815275474, 0.4286513165586879, 0.9642067966077235, 0.2534046915188728, 0.08697751816092071, 0.8792501564264749, 0.629642009566426, 0.6314100395448802, 0.7743277052937813, 0.9104949339617914, 0.840440805697928, 0.5404779055776763, 0.9347773671807053, 0.38755746509272, 0.803369306230527, 0.8966425612886076, 0.7886475139801737, 0.8907941079713984, 0.9190014978832025, 0.3522378332471661, 0.1809014504433939, 0.7336944853537225, 0.679888350179917, 0.1899336275352233, 0.791565555728643, 0.1067866556887754, 0.8860612799729447, 0.9367096223134744, 0.8639495448862111, 0.8782437507986685, 0.8302753492657331, 0.809246382642996, 0.9489076442875167, 0.6454229523694828, 0.04155980960796609, 0.8665041382416315, 0.1619827626792043, 0.5565828858468974, 0.3438258751795431, 0.3942275346898335, 0.9283744290898972, 0.6325830460054775, 0.122929910215236, 0.7522797532502616, 0.8972993534299837, 0.4731648184244552, 0.7708474985702127, 0.1508465096375764, 0.5295553683583388, 0.8547957966471971, 0.7024691755465428, 0.4684299719444062, 0.2244610051764785, 0.06738333747301979, 0.9145680765086048, 0.8503190574296829, 0.8699211983668487, 0.9075726506652723, 0.8125612641935661, 0.1324109903321076, 0.8515026484303992, 0.8666935506701156, 0.9245019813561807, 0.5361574183136518, 0.8308943234035726, 0.7647222555512423, 0.9159763441092864, 0.5190913963288092, 0.8928229399251451, 0.5707529496400237, 0.9343160770300315, 0.2547839947945623, 0.8913151216228844, 0.223496387182918, 0.9013900066737581, 0.126912980063931, 0.0938116230998244, 0.8835051043478275, 0.6624762956118966, 0.6292629647931889, 0.2299240837554979, 0.9695268312861339, 0.2534046915188728, 0.5777582640025832, 0.5191726594909567, 0.9265362606441389, 0.2079933538642454, 0.9349466692539032, 0.3655144546780216, 0.1493401333693624, 0.4664213351146896, 0.5331210003016799, 0.8598519162876399, 0.4720884356129527, 0.8952518575745732, 0.7912019413079115, 0.1429432971101487, 0.7981491417404037, 0.7282408814095576, 0.9567712858079624, 0.8212946734056131, 0.6074315581830233, 0.7856999935768023, 0.1372238635707822, 0.8761504406261441, 0.9040762460981876, 0.9081517064494045, 0.9474670754436387, 0.281231292023929, 0.3390927372020315, 0.9480257660647574, 0.8311989201224447, 0.5366551813586112, 0.9375431236313668, 0.9623354548612517, 0.9580572325538602, 0.5752668110481099, 0.9087426219429084, 0.3468515258883331, 0.7120456179760087, 0.8415949727501237, 0.633421707019731, 0.8728889518506465, 0.8967713999817422, 0.2393218619503596, 0.8909502607437078, 0.9247399939031163, 0.7113741304335964, 0.9516574813231364, 0.6065518446899986, 0.5559651751026748, 0.2462092450152424, 0.5251860236577571, 0.8626393300473802, 0.8553625770855506, 0.4554509237222495, 0.09096122393915286, 0.529780817243299, 0.1132163886582516, 0.6816431744145428, 0.9362134283263105, 0.7412706566370515, 0.9244285156386869, 0.8902138302828968, 0.5906194062496973, 0.8830436003628626, 0.8234964935583747, 0.8823463108045396, 0.8452618508291229, 0.07941357187491897, 0.7357914877268877, 0.4290296557540788, 0.7740804045679049, 0.04487007138865241, 0.03997374347326944, 0.912296929053887],
+ [0.2553998737962824, 0.07631735783024095, 0.07897960011085291, 0.2207949512078856, 0.1016511838719186, 0.3545810650329531, 0.942970225868031, 0.09126771959008544, 0.002046905469766074, 0.004844626977622985, 0.001636702104588283, 0.001975464699602527, 0.002152693042850789, 0.002886097143871596, 0.01079128801224668, 0.0007538852377919047, 0.0001167702235517668, 0.00435688803390722, 5.1002818324778e-05, 0.0001729815043981829, 0.0006733597429191042, 0.0001443357116525265, 0.07385327143180669, 0.0005326734633262727, 0.001075818641876393, 0.05550862949184748, 0.01130092204396166, 0.006479924965262574, 0.1131515866965035, 0.03553527069217096, 0.07275848957278573, 0.001887435176864453, 0.001200647365981756, 0.01863134658795579, 0.001526263597340909, 0.9130181414757098, 0.01529451230761291, 0.07406068052814456, 0.07981696354496427, 0.2235332913352734, 0.08049189368026742, 0.02375572480235134, 0.002419858768391037, 0.03472005251374328, 0.002040716203898256, 0.1956996753012791, 0.05210174980806165, 0.01007955713816182, 0.08751965344976946, 0.07580785714157701, 0.6473777484864973, 0.8190782985420806, 0.0009888467962190556, 0.3173746991954007, 0.8100230708593901, 0.2059874266021218, 0.8932029257335347, 0.03707216917959535, 0.02073986159084442, 0.05640118328947497, 0.1118875137069056, 0.1657372235194127, 0.004306755200965905, 0.02494405362719899, 0.01470587181551327, 1.31347178174259e-05, 0.01265072157945855, 6.372616369940412e-05, 0.003505852925021835, 0.001514115485064287, 0.004276708894825967, 0.03469682994516703, 0.102862828255405, 2.159774127705953e-05, 0.2425074865136805, 0.07643882230721545, 0.5264885468158881, 0.01482016511740909, 0.8491495420529105, 0.0008676286302631026, 0.00395103663354991, 0.01025282755289429, 0.001951938899600739, 0.0004129809964198562, 0.9326150727325982, 0.07482081888756961, 0.08063891833366137, 0.007803525559271599, 0.08299124096650871, 0.01176323345165673, 0.0001148391665040469, 0.1415442010888649, 0.1184510092537426, 0.06488130463577248, 0.001550345475611415, 0.1621292281987863, 0.006434883592133867, 0.0390944435218161, 0.001627184406719129, 0.02695925261158226, 0.002018274757312532, 0.02381130151757035, 0.0003784733668262425, 0.004533273133334742, 0.0006394216911327579, 0.05707727078425542, 3.43117576046495e-05, 3.507664767224504e-05, 0.1091002579265486, 0.008836026438070649, 0.3677294436546928, 0.0004060643436808472, 0.01575162869039373, 0.001526263597340909, 0.4219583389755819, 0.005542578428455856, 0.005739546293110378, 0.0003624399383724484, 0.01736517527853375, 0.0008387460506655657, 4.277324451437318e-05, 0.0002700419616530316, 0.006712592937335689, 0.01028954029981052, 0.002030807924387894, 0.09983720766549499, 0.2034716659023486, 0.0001644672248535993, 0.02373313968558726, 0.009860080906007207, 0.0227960413734721, 0.02732853212541473, 0.002407184545829678, 0.01262385153017814, 3.874491145169847e-05, 0.0386658754248187, 0.009490169270680476, 0.03557873332422891, 0.04048929922354462, 0.7186559291889745, 0.6608153875038184, 0.02284045048769326, 0.1643459715101531, 0.4629114428923355, 0.0520022778318248, 0.00880261940483151, 0.02815401462621663, 0.005636571493453016, 0.002225131068309814, 0.0005875629986705686, 0.2871815978825973, 0.009960093789229935, 0.001978717880497971, 0.01954337296283469, 0.05074400224223814, 0.0001119556755373595, 0.01697913254226044, 0.02257472162772266, 0.2876662719239387, 0.03032576686210087, 0.3930484182499576, 0.003794690851895586, 0.0006771744930604194, 0.007190580867317107, 0.1309916798306492, 0.02650961718268966, 0.5444148300203245, 0.0001369692775655127, 0.4697846564030937, 2.614494296533173e-05, 0.007232856266002665, 0.0412637181315732, 0.007473307120980099, 0.05287411942419848, 0.10281142388182, 0.4081340340910627, 0.01508529183000272, 0.1746159553524696, 0.005358535051338847, 0.1515801234952836, 9.36372282825981e-05, 0.00127450690507435, 0.001925188529169687, 0.01002087345566931, 1.656111121114513e-05, 2.628855622720807e-06, 0.05898063972005398]
+ ],
+ "analysis":{
+ "authors":"Sergei L Kosakovsky Pond",
+ "citation":"*Gene-wide identification of episodic selection*, Mol Biol Evol. 32(5):1365-71",
+ "contact":"spond@temple.edu",
+ "info":"BUSTED (branch-site unrestricted statistical test of episodic diversification) uses a random effects branch-site model fitted \njointly to all or a subset of tree branches in order to test for alignment-wide evidence of episodic diversifying selection. \nAssuming there is evidence of positive selection (i.e. there is an omega > 1), BUSTED will also perform a quick evidence-ratio \nstyle analysis to explore which individual sites may have been subject to selection. v2.0 adds support for synonymous rate variation, \nand relaxes the test statistic to 0.5 (chi^2_0 + chi^2_2). Version 2.1 adds a grid search for the initial starting point.\nVersion 2.2 changes the grid search to LHC, and adds an initial search phase to use adaptive Nedler-Mead. Version 3.0 implements the option\nfor branch-site variation in synonymous substitution rates\n",
+ "requirements":"in-frame codon alignment and a phylogenetic tree (optionally annotated with {})",
+ "version":"3.0"
},
"background":0,
- "fits":{
- "Nucleotide GTR":{
- "Log Likelihood":-3531.963798530155,
- "estimated parameters":24,
- "AIC-c":7112.142458295762,
- "Equilibrium frequencies":[
- [0.3563279857397504],
- [0.1837789661319073],
- [0.2402852049910873],
- [0.2196078431372549]
- ],
- "Rate Distributions":{
- "Substitution rate from nucleotide A to nucleotide C":0.5474490057204714,
- "Substitution rate from nucleotide A to nucleotide G":1,
- "Substitution rate from nucleotide A to nucleotide T":0.2645352969683238,
- "Substitution rate from nucleotide C to nucleotide G":0.4863078374555331,
- "Substitution rate from nucleotide C to nucleotide T":1.018028772244997,
- "Substitution rate from nucleotide G to nucleotide T":0.3025951149895378
- },
- "display order":0
- },
- "MG94xREV with separate rates for branch sets":{
- "Log Likelihood":-3466.725508616141,
- "estimated parameters":31,
- "AIC-c":6996.530451399855,
- "Equilibrium frequencies":[
- [0.04785168648208005],
- [0.03911346079312019],
- [0.04842054060317301],
- [0.04069665666515385],
- [0.01817010744778396],
- [0.01485205303123071],
- [0.01838611113045968],
- [0.01545321970309948],
- [0.0190138898893362],
- [0.01554175184587827],
- [0.01923992433904378],
- [0.01617083546230154],
- [0.02796925133965702],
- [0.02286176927319543],
- [0.02830174586718859],
- [0.02378714529482007],
- [0.01687870337957799],
- [0.01379647304851128],
- [0.01707935503225849],
- [0.01435491300079667],
- [0.006409133648843443],
- [0.005238757839512795],
- [0.006485324528555602],
- [0.005450807083377185],
- [0.006706760641638982],
- [0.005482034985409045],
- [0.006786489669196017],
- [0.005703931360295163],
- [0.009865581170012171],
- [0.008064021368173151],
- [0.009982861811889655],
- [0.008390428826966174],
- [0.03287895020631181],
- [0.02687490503171972],
- [0.033269810543681],
- [0.0279627207822247],
- [0.01248470225271473],
- [0.01020486315060615],
- [0.01263311863778268],
- [0.01061792547971484],
- [0.01306446616325414],
- [0.01067875601941112],
- [0.01321977470017749],
- [0.01111100011404158],
- [0.01921770557551369],
- [0.01570834862514353],
- [0.01944616295744266],
- [0.01634417558076203],
- [0.01975257768318274],
- [0.02055210293142003],
- [0.009176034326710849],
- [0.007500393094996483],
- [0.00928511773266342],
- [0.007803986567571961],
- [0.00784869593340758],
- [0.009716299514778986],
- [0.008166387662818644],
- [0.01412467213650941],
- [0.01154535713247913],
- [0.01429258425298098],
- [0.01201267864744234]
- ],
- "Rate Distributions":{
- "non-synonymous/synonymous rate ratio for *test*":[
- [0.9970623081401093, 1]
- ]
- },
- "display order":1
- },
- "Unconstrained model":{
- "Log Likelihood":-3437.188861487313,
- "estimated parameters":35,
- "AIC-c":6945.751768776152,
- "Rate Distributions":{
- "Test":{
- "0":{
- "omega":0.1052869846173941,
- "proportion":0.2379046712842726
- },
- "1":{
- "omega":0.2107329369900513,
- "proportion":0.4121351840538361
- },
- "2":{
- "omega":3.951290720456698,
- "proportion":0.3499601446618912
- }
- }
- },
- "display order":2
- },
- "Constrained model":{
- "Log Likelihood":-3459.576322342121,
- "estimated parameters":34,
- "AIC-c":6988.449647409037,
- "Rate Distributions":{
- "Test":{
- "0":{
- "omega":0,
- "proportion":0.1368169359858254
- },
- "1":{
- "omega":0,
- "proportion":0.09947859848803366
- },
- "2":{
- "omega":1,
- "proportion":0.7637044655261409
- }
- }
- },
- "display order":3
- }
- },
- "timers":{
- "Overall":{
- "timer":79,
- "order":0
- },
- "Preliminary model fitting":{
- "timer":22,
- "order":1
- },
- "Unconstrained BUSTED model fitting":{
- "timer":29,
- "order":2
- },
- "Constrained BUSTED model fitting":{
- "timer":18,
- "order":3
- }
- },
- "Site Log Likelihood":{
- "unconstrained":[
- [-9.761780003252589, -3.556981916965661, -3.871692954311539, -17.99295796244379, -17.6956827873063, -30.01736049845984, -32.80456708119989, -24.24615674389706, -17.22716501528761, -10.63078274532717, -17.5513791952437, -23.10676596882748, -20.1589722777239, -16.08007905666529, -22.07489132346995, -13.27698585999586, -11.57373969856821, -15.0218610811265, -12.31301984930962, -9.878172230255872, -9.283873417740052, -12.8230707251624, -24.29926852464868, -14.11614921655551, -14.80291769006257, -14.24359374301642, -21.23808978297999, -15.20669497937926, -21.11914571105627, -18.695897789747, -22.4289474056158, -14.71510620919697, -10.95989097579746, -28.25520114439835, -7.114758548777005, -35.1823654002276, -15.94120703275923, -4.330001696693314, -4.810804241726376, -24.36449596493429, -19.85422544995369, -20.21977077882305, -12.00277035613209, -19.6600724196642, -15.22159826235479, -24.22386090964918, -16.83876198375444, -15.39919245352698, -20.55491461157309, -23.30374279272433, -29.43636445622652, -31.41899626907746, -20.08375283223842, -21.69892250748334, -31.28859827841539, -26.08296126442238, -28.95584777914672, -20.97050845715194, -22.87836756552637, -16.10418205553547, -21.63783799404863, -22.29130394316017, -18.35819291264508, -23.0059705707678, -14.03484863809933, -9.416359563812415, -18.79111063130158, -12.78164205666208, -11.19294341786628, -10.24271903306927, -9.811969009737055, -20.99099337931294, -5.038213419512006, -12.36951590374203, -23.75822209792559, -24.38317903225788, -29.79314521637115, -15.03360351335341, -30.15269907145897, -15.40303952466706, -22.87293615165179, -10.81368963977958, -12.47042186757648, -11.73824102802078, -34.62663852693693, -22.96333978037858, -16.64020476652507, -18.34587549890907, -24.44431984136763, -15.73196577376136, -10.85174956948496, -20.76376393713096, -22.87186260864842, -24.188197096568, -13.78231255943875, -23.02551088711758, -13.64118597104227, -23.70873447722415, -13.43680638220221, -18.36670985939329, -14.24443250362629, -20.74306008601751, -11.19634482669214, -20.60160418194348, -11.398502668876, -23.3132179060432, -12.41458242767006, -8.59839648909502, -21.13421524691898, -18.70680195104232, -24.04441379518424, -9.992102259489076, -22.86252385976109, -7.114758548777005, -27.5565726745568, -12.87223741705519, -24.48854177549546, -9.791375505313344, -21.57931931289719, -13.73761157881194, -12.7003636235767, -15.92686724109126, -13.25111195536186, -19.5598880256505, -12.78420433838847, -25.3479232600814, -23.21813833324584, -11.87082416732899, -18.34124875195977, -13.39208375265505, -23.22887768380001, -13.67243009919361, -12.64371510970045, -15.23267340039615, -12.46602644865305, -15.78570032614895, -20.49430844113086, -16.74759955468868, -21.37629168953962, -31.91852172562975, -32.91408279059539, -28.11259733944721, -23.28467231775043, -25.08348256456863, -24.36722240264622, -27.85361506098191, -22.81200431380501, -12.06099437357067, -21.72512567277257, -14.75966862326406, -26.55673909887922, -15.9891326482062, -16.67305867563187, -15.89127092598368, -17.11654012165223, -15.14718002836891, -19.22179155508141, -20.14784462411578, -27.16144224004015, -22.80088235078308, -29.6346258900827, -14.87414990449581, -10.09001804965354, -14.06722825110506, -21.55226091029841, -17.89237433412178, -26.9887399484436, -7.247032599266484, -29.10107988545393, -11.92987823423617, -14.41471074589252, -20.22815853097579, -13.94727875575511, -24.40018676619344, -24.57667974105677, -29.23515533817404, -18.36670890820324, -29.22340700233682, -17.74018014861057, -26.54152667547728, -8.953815058919133, -20.2800904930613, -14.09345734559062, -14.03391364104814, -9.421270195111878, -9.469430414396884, -20.11488196129918]
- ],
- "constrained":[
- [-10.85606152021318, -3.471229863506585, -3.800029997251122, -19.76181202731181, -18.99505347406228, -33.70672014040629, -40.08617973771972, -28.08241530494764, -19.10728836136312, -9.985069679724274, -15.75689438367687, -24.2738510731431, -19.60585366503884, -16.3091575384683, -22.29810643714523, -11.58047190013798, -10.65369978272362, -15.34194795652741, -10.92534862913859, -8.262063009605756, -7.795056828277495, -10.98823292846032, -26.45715781872953, -13.56039498470006, -14.80733027279041, -14.97339798653168, -22.83819293785454, -15.99960324964237, -23.05374383928736, -18.64540846688676, -22.52507508510511, -14.06096141784007, -9.950850202190837, -31.09994454740333, -5.657479911616817, -40.20764738574088, -15.24880713029523, -4.245259501823234, -4.75823140493186, -26.42921606238378, -21.05932496028346, -21.24380652339677, -12.51510927509652, -19.4431274563198, -13.45707855557425, -27.34067162541028, -16.92068505165836, -15.27874830129921, -21.78078086811648, -25.74988026772384, -32.3591534741427, -36.92136999297909, -20.86637747607929, -26.21690123953934, -38.38842669761863, -29.5707349344923, -34.78024872766768, -22.34647319638493, -24.42164357523894, -15.89813120477618, -24.88114938112022, -24.16882658381608, -19.15062432752575, -25.32782323726632, -12.54397568681377, -7.658560467541037, -20.06316291990198, -11.38834848993708, -10.34978442983486, -8.798066094581541, -8.365525022998657, -23.37022898655908, -5.038213419512005, -11.73698294324726, -26.59271763114307, -27.51600374427774, -33.19580365368542, -14.08391822294567, -37.61485496561196, -14.61037124768515, -24.95712121575756, -9.468302677820519, -11.80724915343188, -10.17626631190552, -39.82223560997122, -23.22993675058718, -15.29814440122603, -18.59041764178898, -25.85430435634182, -16.63728997890176, -9.088390872315317, -23.36486681955814, -25.10120831076364, -26.87850226687513, -12.5163839486935, -25.46276168897045, -13.30043078187602, -26.00037628519058, -12.36183639601969, -19.32639068670407, -13.90921600814463, -23.30517706031209, -10.38197265044853, -21.48132876823857, -10.34226801788524, -25.48737661714055, -11.54862505674196, -7.268129324767196, -23.12171070541123, -16.87868227611221, -26.86559749366134, -8.472693915554212, -26.90473561049812, -5.657479911616817, -30.14077517350693, -11.1338558936567, -26.90933331018406, -8.683054657060978, -22.93750465468248, -12.09242051639567, -12.24278260635322, -16.46214458935806, -11.52233069441597, -19.57563980700768, -11.24562305579595, -28.73517189370709, -26.5995022362575, -10.11077097725237, -17.64257519637804, -12.22627059873072, -25.794387889477, -13.00339712214579, -11.44442645621986, -15.23294312487709, -11.01984685521603, -15.23436625095256, -21.84913978769858, -17.43830973910884, -24.04200658810043, -36.02241585126664, -39.74114047148559, -30.51107839063483, -25.24778323303905, -29.10134605686299, -27.4051878646382, -29.40431078055861, -26.00565963206897, -11.37219430365775, -23.62588495555996, -13.84835203928034, -30.39496528205261, -17.46875631982503, -16.48393583594229, -16.95840797360417, -18.18414725855796, -14.60783644912805, -20.36574492127523, -22.08905835390395, -30.09377992258299, -24.20776345765027, -33.87407556904575, -13.85334118326135, -9.038547460214009, -12.31883826587824, -23.76076017501662, -16.13507283064812, -31.74425687978529, -5.621431190076298, -32.77926379309199, -10.93320737320503, -14.18712500350103, -23.00952178187488, -13.74809094768596, -27.13572996742387, -27.80389794085873, -33.12824566268318, -18.82222585779942, -32.59467769783617, -18.82117621115135, -28.87355399347379, -7.202495413751149, -20.10273643846979, -13.55384673130033, -13.92541401636034, -7.622924396558326, -8.028485273604586, -20.99338693632994]
- ],
- "optimized null":[
- [-9.984891074365004, -3.552861592101205, -3.869898855143417, -18.01518487110813, -17.38504309777226, -29.7102253995114, -33.97262688823771, -25.58952900757811, -18.32327569996284, -10.43679078115309, -17.34797699860558, -23.44071853477707, -20.13369389964067, -16.23209205498968, -20.84681207056716, -13.14211233137375, -11.68410006052765, -15.49850331840433, -12.80349920668154, -9.951696917262908, -9.674794006047554, -13.35878598779897, -23.86875827725563, -13.92120845548608, -15.25915378398707, -14.40626012443236, -21.26593666732801, -15.47805189201786, -20.8967440084538, -17.92205772755303, -21.52612599164656, -14.37849206841925, -11.28236683284286, -27.85944578501297, -7.045007615754844, -35.50167243235479, -15.43207104477209, -4.330649700739783, -4.821509537453836, -24.61117309405466, -19.66210749973598, -19.61978108110112, -13.06931658869425, -18.90379736902437, -15.17248506099829, -24.20575482256608, -16.80670782290678, -15.1069403318206, -20.23445804273289, -22.93238636351499, -28.6422792678352, -31.91671871385733, -19.7070935797896, -24.16184701754757, -32.87373578813684, -25.97502236883938, -30.04305670719911, -20.66008132977401, -22.5476319199698, -15.71574496122768, -21.82260087605331, -22.33213004101708, -17.88649192977146, -22.85979453942399, -13.9142190617628, -10.20989813642594, -19.67318749886311, -13.22545647691756, -11.35738362057711, -10.37800058317319, -9.86308947602663, -20.98168478524144, -5.038213419512004, -12.8612703045419, -23.7103757747438, -25.78805046306136, -29.5117411496098, -15.02489637507387, -32.51478386333478, -15.48689562410333, -23.58179278538965, -10.7011656905293, -12.18338021676437, -11.80719456318334, -34.37559964635795, -21.96698531834351, -15.96606915985646, -18.18645503653203, -23.73685168133605, -15.7426553469114, -11.56446818066272, -21.42813665189797, -23.10666793730778, -24.26053675245742, -14.08444644301535, -23.12886976791419, -13.54997092114479, -24.18202649171034, -13.43311848775762, -18.68125871223531, -14.34963037446899, -21.30807004664649, -11.23675042114956, -20.25521737033718, -11.41928014036639, -23.0616314567799, -12.74836397165115, -8.946938971416877, -21.33592841357732, -18.29022453494306, -23.78096262851221, -10.26615870794974, -23.87195921412485, -7.045007615754844, -27.36975377176551, -13.02213773679562, -24.88461586299227, -9.937370797941819, -20.9215542254461, -13.7430158107626, -13.32781861737069, -16.57378722435969, -13.1562876406111, -18.65461183747465, -12.88434508060274, -25.53251613794421, -23.47076517726, -12.38103504563448, -18.08858152438308, -13.3986078002421, -24.83005553415067, -13.48186232123563, -12.76305322156708, -14.99349220446663, -12.68915386346622, -15.16813193431097, -20.38979714624436, -17.1398617656887, -21.99353054090562, -31.80290581785966, -34.17165493312128, -28.14103833717329, -23.01519425280903, -25.32718282655863, -24.9256764033518, -27.36738567584731, -23.63994953138027, -12.19474154438638, -21.8509764153975, -14.27265880961605, -27.81140090827595, -16.66595175805092, -15.90073698436111, -16.04898816099204, -16.77891193093655, -15.05041271240863, -18.6937096770671, -20.92753847593657, -26.68202074910777, -22.68645320525759, -30.02139727511975, -14.61774067439237, -10.02271219166692, -14.02556111130297, -22.35631047609814, -17.23179491687371, -27.80786897153735, -7.71222261637312, -29.01667081229076, -12.42383366521858, -14.96109424540947, -20.51828142366711, -13.95474218677742, -25.26930987352585, -25.30942633816443, -29.95264501627203, -17.87797633090322, -29.28864522431501, -18.28270560387423, -26.07314333903045, -9.265582530948477, -19.57038320696334, -13.84155482021799, -13.76410195180156, -10.09880900833976, -10.13770828948875, -20.68018631936204]
- ]
- },
- "Evidence Ratios":{
- "constrained":[
- [2.987035777683669, 0.9178217737437788, 0.9308445775388399, 5.864129597495543, 3.666988257062931, 40.01921212564599, 1453.329858192022, 46.3517274521344, 6.554313261152158, 0.5242885566486172, 0.1662130613392027, 3.212614540819785, 0.5751533301022933, 1.257440721352396, 1.250089456152151, 0.1833214774704383, 0.3985031341778748, 1.377247408059552, 0.2496560220961017, 0.1986701791114262, 0.2256395217898774, 0.159639393704319, 8.652854738603175, 0.5736394408536711, 1.004422332506298, 2.074674436945399, 4.953543380186865, 2.209813825803168, 6.921262036590584, 0.9507640800590974, 1.100899617321825, 0.5198864839379664, 0.3645685156450084, 17.19714536690562, 0.2328691346279994, 152.2131719709853, 0.5003737786888893, 0.9187491121066572, 0.9487852120654622, 7.883091091521568, 3.337091136584989, 2.784409283932767, 1.669190734679053, 0.8049742711776068, 0.1712690260857312, 22.57426895337745, 1.085372306650974, 0.8865265964983139, 3.407116241547518, 11.54367277296439, 18.59307162257273, 245.2734532644677, 2.187205373636184, 91.65016109978839, 1211.759142055416, 32.71303656181449, 338.4583183795538, 3.958894181734716, 4.679896572127406, 0.8137916933052433, 25.61841393034561, 6.537289569530828, 2.208760315392158, 10.19454391110528, 0.2251760020370068, 0.1724239350018968, 3.568167963566551, 0.2482563079467741, 0.4303489068500915, 0.2358279091453541, 0.2354059080062318, 10.79664683030406, 0.9999999999999982, 0.5312444740983824, 17.02181119579284, 22.93868328909911, 30.04386370541763, 0.3868627537181412, 1740.897204618787, 0.4526354258455894, 8.038038325908458, 0.2604389084082438, 0.5152141115456746, 0.209721521558208, 180.4758697127573, 1.305514179179812, 0.2613067262507715, 1.277036479085304, 4.095891978587106, 2.472733466018775, 0.1714679865462201, 13.4785951464023, 9.293783187007939, 14.73617227655005, 0.2819773273497369, 11.44154239787743, 0.7112330044400204, 9.891163748924974, 0.341307999103254, 2.610863024250461, 0.715183235651846, 12.96323111519599, 0.4429173141007886, 2.410235803025134, 0.3477627964575015, 8.794783055600073, 0.4206486430093566, 0.2644066118480111, 7.29723462938499, 0.1607154811869344, 16.79672116274557, 0.2188413274550005, 56.95216760630651, 0.2328691346279994, 13.2527158196516, 0.1758047062874589, 11.25476432648051, 0.3301128054448652, 3.889129453787352, 0.1929756888698665, 0.6328125582337467, 1.707921865741156, 0.1775006051199708, 1.015876494623396, 0.2146854634782269, 29.58444254980177, 29.41085732710528, 0.1720357129869316, 0.4972444336487338, 0.3116691239926225, 13.00729307176291, 0.5122036510611201, 0.3014085415888103, 1.00026976085985, 0.2354681559800242, 0.5761806291357867, 3.876107182723861, 1.995131941849157, 14.37822484490952, 60.57571835920439, 922.4726067466381, 11.00644544990011, 7.121446858825492, 55.58222702294439, 20.86275396084217, 4.714749185132652, 24.37737183652841, 0.50217828651945, 6.690972854579194, 0.4019946158005773, 46.44301992158756, 4.391292801814232, 0.8276848279024352, 2.907044843855059, 2.908411735743323, 0.5831309060013494, 3.139154092062445, 6.967202141660374, 18.77146096245092, 4.083200457885609, 69.36966574602748, 0.3603034372761033, 0.3494235125609156, 0.1740539474113665, 9.102046375934606, 0.1725097532596096, 116.2237173206706, 0.1967932863167221, 39.57445790025699, 0.3691062038535791, 0.7964541286880364, 16.14101020285773, 0.8193959897025127, 15.41811630139388, 25.20943173776431, 49.06227082795505, 1.576988395869989, 29.11550049727357, 2.947614097314125, 10.29879932442459, 0.1735447747495909, 0.8374832172472122, 0.5829752104000613, 0.8971792315392203, 0.1655725521668218, 0.2367039343819634, 2.407298044116152]
- ],
- "optimized null":[
- [1.249959400407102, 0.9958881520275259, 0.998207509265751, 1.022475766760606, 0.7329779279148643, 0.7355512219978014, 3.215747411518881, 3.831944066897763, 2.992504567232528, 0.8236645230667027, 0.8159500030737468, 1.396476901447714, 0.9750384449114691, 1.16417536866286, 0.2928545373193804, 0.8738264187311083, 1.116680407100678, 1.610657107893188, 1.633098870338358, 1.076295106848796, 1.478341111181925, 1.708669953055735, 0.6501772588199817, 0.8228834033449909, 1.578122886012883, 1.176644073870286, 1.028238233000157, 1.311743164559289, 0.8005936991596435, 0.4612384787800625, 0.4054241751261601, 0.7141843613652971, 1.380541560105011, 0.6731713608501634, 0.932626077339456, 1.376173789613603, 0.6010146384105997, 1.000648214046449, 1.010762802431324, 1.279765846941387, 0.8252095291075795, 0.5488172901332377, 2.905327825256244, 0.4694117092940189, 0.952073347603641, 0.9820568432858974, 0.9684541283622321, 0.7465802831481059, 0.725817575723242, 0.6897980335692911, 0.4519945356959116, 1.644970489890064, 0.6861498379435136, 11.73909248217663, 4.87996237464428, 0.8976824471171899, 2.965984233784409, 0.733133747843722, 0.7183950548657764, 0.6781158778869135, 1.202933169206003, 1.041670940984456, 0.6239400537888191, 0.864005597730941, 0.8863622283336499, 2.211207115702391, 2.415912028974954, 1.558641206543682, 1.178733082401182, 1.144859074170125, 1.052449670353621, 0.9907345967710618, 0.9999999999999973, 1.635182470378155, 0.9532802729006801, 4.075002787751862, 0.7547233152543775, 0.9913306590671749, 10.61305441401069, 1.087472394658304, 2.031666990662131, 0.8935759463782673, 0.7504804700650514, 1.07138642619565, 0.7779921221867564, 0.3692230071631759, 0.5095967222916621, 0.852637781481885, 0.492890538993211, 1.010746910759831, 2.039528413292879, 1.943271153632765, 1.264662551213628, 1.075020419076957, 1.352742324566819, 1.108889296748787, 0.9128213876445376, 1.605270076656883, 0.9963188974862515, 1.369641261789208, 1.110930409345364, 1.759465308015671, 1.041233006895448, 0.7072388659882123, 1.020994825899436, 0.7775662346759626, 1.396238093640341, 1.417000739126258, 1.223497018037751, 0.6592994704264704, 0.7683951448151665, 1.315289046185217, 2.744051160985256, 0.932626077339456, 0.8295939599329692, 1.161718436561281, 1.485979405967741, 1.157190740711233, 0.5180077437805523, 1.005418861153479, 1.872838124227439, 1.909650007781456, 0.9095327119137432, 0.4044301708455042, 1.105326473224138, 1.202728682967098, 1.287402785135559, 1.665642405761295, 0.7767263119192113, 1.006545375541812, 4.958869792471186, 0.8264897380438972, 1.126750821714303, 0.7872722189265667, 1.249979829536444, 0.5392540993266187, 0.900764623315236, 1.480325818230283, 1.853802344884983, 0.8908173136045756, 3.516872648338504, 1.028849304595149, 0.7637780328545294, 1.275961818909257, 1.7479680529214, 0.6149407328711725, 2.288611307253957, 1.143103773111974, 1.134112880938005, 0.6144610028110447, 3.50665225694476, 1.967609019313462, 0.4619393418252924, 1.170835076724906, 0.713460509830789, 0.907767204501339, 0.5897350692995594, 2.180804513956808, 0.6191414671741319, 0.8918751295230388, 1.472219881303941, 0.7738252314079443, 0.9349092081542767, 0.9591890032827355, 2.234571675884028, 0.5165519486568414, 2.268523145559755, 1.592316727559848, 0.9190552183615908, 1.63878552010542, 1.726996028513171, 1.33659173528842, 1.007491351842102, 2.384818706326968, 2.080787852232155, 2.049282389773126, 0.6134033430403113, 1.067413275400906, 1.720346037637947, 0.6260135038640929, 1.365837060781729, 0.4917881296168616, 0.7773205034026993, 0.7635232604405103, 1.969025623887814, 1.950874776061578, 1.759983366341118]
- ]
- },
- "tested":{
- "0":{
- "Pig":"test",
- "Cow":"test",
- "Node3":"test",
- "Horse":"test",
- "Cat":"test",
- "Node2":"test",
- "RhMonkey":"test",
- "Baboon":"test",
- "Node9":"test",
- "Human":"test",
- "Chimp":"test",
- "Node12":"test",
- "Node8":"test",
- "Node1":"test",
- "Rat":"test",
- "Mouse":"test"
- }
- },
- "data partitions":{
- "0":{
- "name":"busted.filter.default",
- "coverage":[
- [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186]
- ]
- }
- },
"branch attributes":{
"0":{
- "Human":{
- "original name":"Human",
- "Nucleotide GTR":0,
- "MG94xREV with separate rates for branch sets":0,
- "unconstrained":0,
- "constrained":0
- },
- "Chimp":{
- "original name":"Chimp",
- "Nucleotide GTR":0.001818647577470898,
- "MG94xREV with separate rates for branch sets":0.001828142895085465,
- "unconstrained":0.001835079043904073,
- "constrained":0.001827227299324197
- },
"Baboon":{
+ "MG94xREV with separate rates for branch sets":0.001771850913718116,
+ "Nucleotide GTR":0.00167976779100812,
+ "constrained":0.0005055252388761481,
"original name":"Baboon",
- "Nucleotide GTR":0.001683434956773037,
- "MG94xREV with separate rates for branch sets":0.001771624553208579,
- "unconstrained":0.001852571561323465,
- "constrained":0.001757260248005238
- },
- "RhMonkey":{
- "original name":"RhMonkey",
- "Nucleotide GTR":0.003773669075849421,
- "MG94xREV with separate rates for branch sets":0.003717699096857038,
- "unconstrained":0.003672835047422234,
- "constrained":0.00373144096412681
- },
- "Cow":{
- "original name":"Cow",
- "Nucleotide GTR":0.2483322373763571,
- "MG94xREV with separate rates for branch sets":0.2480141631033857,
- "unconstrained":0.2960120156157274,
- "constrained":0.2592686681333873
- },
- "Pig":{
- "original name":"Pig",
- "Nucleotide GTR":0.187244836750842,
- "MG94xREV with separate rates for branch sets":0.1926081878751187,
- "unconstrained":0.2187526946336905,
- "constrained":0.1943776301130502
- },
- "Horse":{
- "original name":"Horse",
- "Nucleotide GTR":0.2091766851769093,
- "MG94xREV with separate rates for branch sets":0.2111575880588217,
- "unconstrained":0.2572135566477119,
- "constrained":0.218486450878766
+ "unconstrained":0.0005398732671668005
},
"Cat":{
+ "MG94xREV with separate rates for branch sets":0.2738959056554072,
+ "Nucleotide GTR":0.266075486389923,
+ "constrained":0.1152712488116292,
"original name":"Cat",
- "Nucleotide GTR":0.266381043956941,
- "MG94xREV with separate rates for branch sets":0.273601177885004,
- "unconstrained":0.3292215104251173,
- "constrained":0.28483085314287
+ "unconstrained":0.120218071527276
+ },
+ "Chimp":{
+ "MG94xREV with separate rates for branch sets":0.001827968855137289,
+ "Nucleotide GTR":0.001817801565830578,
+ "constrained":0.0006181497274348637,
+ "original name":"Chimp",
+ "unconstrained":0.0006183542388399873
+ },
+ "Cow":{
+ "MG94xREV with separate rates for branch sets":0.2477119781238836,
+ "Nucleotide GTR":0.2480176045457076,
+ "constrained":0.1036665344622347,
+ "original name":"Cow",
+ "unconstrained":0.1088268022245659
+ },
+ "Horse":{
+ "MG94xREV with separate rates for branch sets":0.211203801568566,
+ "Nucleotide GTR":0.2090856782081004,
+ "constrained":0.08236651201101133,
+ "original name":"Horse",
+ "unconstrained":0.08564084427400141
+ },
+ "Human":{
+ "MG94xREV with separate rates for branch sets":0,
+ "Nucleotide GTR":0,
+ "constrained":0,
+ "original name":"Human",
+ "unconstrained":0
},
"Mouse":{
+ "MG94xREV with separate rates for branch sets":0.1200702443392807,
+ "Nucleotide GTR":0.1181301915748399,
+ "constrained":0.04601717170435755,
"original name":"Mouse",
- "Nucleotide GTR":0.1181831744338598,
- "MG94xREV with separate rates for branch sets":0.1201847378516324,
- "unconstrained":0.1489713993010398,
- "constrained":0.1233480139851019
- },
- "Rat":{
- "original name":"Rat",
- "Nucleotide GTR":0.06669700444436912,
- "MG94xREV with separate rates for branch sets":0.0670850471739789,
- "unconstrained":0.07366345007817726,
- "constrained":0.06713082546371778
+ "unconstrained":0.04942545223877414
},
"Node1":{
- "Nucleotide GTR":0.276880831396131,
- "MG94xREV with separate rates for branch sets":0.2843521449765504,
- "unconstrained":0.459085769955035,
- "constrained":0.3115534692518958
+ "MG94xREV with separate rates for branch sets":0.2837967450491412,
+ "Nucleotide GTR":0.2767871391397028,
+ "constrained":0.1295742765519239,
+ "unconstrained":0.1515367890887531
},
"Node12":{
- "Nucleotide GTR":0.01783434870161725,
- "MG94xREV with separate rates for branch sets":0.01788794906051452,
- "unconstrained":0.01828498503175797,
- "constrained":0.01770410398930177
+ "MG94xREV with separate rates for branch sets":0.01788296579298991,
+ "Nucleotide GTR":0.01784443144961206,
+ "constrained":0.005338125135456628,
+ "unconstrained":0.00572208893382143
},
"Node2":{
- "Nucleotide GTR":0.06617535490721377,
- "MG94xREV with separate rates for branch sets":0.06447679597474805,
- "unconstrained":0.0623969317369398,
- "constrained":0.06097949807503514
+ "MG94xREV with separate rates for branch sets":0.06423714540466627,
+ "Nucleotide GTR":0.06616183769400197,
+ "constrained":0.02253286838656328,
+ "unconstrained":0.02248978054488407
},
"Node3":{
- "Nucleotide GTR":0.09884524766349881,
- "MG94xREV with separate rates for branch sets":0.1017497956116402,
- "unconstrained":0.1285021744856729,
- "constrained":0.1065011238088613
+ "MG94xREV with separate rates for branch sets":0.1017201477652066,
+ "Nucleotide GTR":0.09890202668045614,
+ "constrained":0.04280347934583096,
+ "unconstrained":0.04618990784049085
},
"Node8":{
- "Nucleotide GTR":0.1061610073141143,
- "MG94xREV with separate rates for branch sets":0.1093806684969149,
- "unconstrained":0.1348034716617685,
- "constrained":0.1118205234697939
+ "MG94xREV with separate rates for branch sets":0.1096720572321177,
+ "Nucleotide GTR":0.10624077635158,
+ "constrained":0.04415239867414091,
+ "unconstrained":0.04768889036449767
},
"Node9":{
- "Nucleotide GTR":0.02568007351415409,
- "MG94xREV with separate rates for branch sets":0.02593963430985144,
- "unconstrained":0.02761127562964508,
- "constrained":0.02639493109700932
+ "MG94xREV with separate rates for branch sets":0.02591275475412757,
+ "Nucleotide GTR":0.02566524291670843,
+ "constrained":0.00997308939110993,
+ "unconstrained":0.009841415288506062
+ },
+ "Pig":{
+ "MG94xREV with separate rates for branch sets":0.1928073761020463,
+ "Nucleotide GTR":0.1871746592118726,
+ "constrained":0.07816490289585476,
+ "original name":"Pig",
+ "unconstrained":0.08275992348314189
+ },
+ "Rat":{
+ "MG94xREV with separate rates for branch sets":0.06698958986289986,
+ "Nucleotide GTR":0.06656862018951525,
+ "constrained":0.02277034233250765,
+ "original name":"Rat",
+ "unconstrained":0.02372534359054489
+ },
+ "RhMonkey":{
+ "MG94xREV with separate rates for branch sets":0.003717482368324115,
+ "Nucleotide GTR":0.003775504255522691,
+ "constrained":0.001359450941376631,
+ "original name":"RhMonkey",
+ "unconstrained":0.00132482447204072
}
},
"attributes":{
- "original name":{
- "attribute type":"node label",
- "display order":0
- },
- "Nucleotide GTR":{
- "attribute type":"branch length",
- "display order":0
- },
"MG94xREV with separate rates for branch sets":{
"attribute type":"branch length",
"display order":1
},
- "unconstrained":{
+ "Nucleotide GTR":{
"attribute type":"branch length",
"display order":0
},
"constrained":{
"attribute type":"branch length",
"display order":1
+ },
+ "original name":{
+ "attribute type":"node label",
+ "display order":0
+ },
+ "unconstrained":{
+ "attribute type":"branch length",
+ "display order":0
}
}
},
+ "data partitions":{
+ "0":{
+ "coverage": [
+[0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186]
+ ],
+ "name":"busted.filter.default"
+ }
+ },
+ "fits":{
+ "Constrained model":{
+ "AIC-c":6918.851822592964,
+ "Log Likelihood":-3419.573452280089,
+ "Rate Distributions":{
+ "Synonymous site-to-site rates":{
+ "0":{
+ "proportion":0.3289898788632067,
+ "rate":0.3124849036133048
+ },
+ "1":{
+ "proportion":0.5748197734913485,
+ "rate":1.039520868895482
+ },
+ "2":{
+ "proportion":0.09619034764544485,
+ "rate":3.115265578623139
+ }
+ },
+ "Test":{
+ "0":{
+ "omega":0,
+ "proportion":0.02093092071081848
+ },
+ "1":{
+ "omega":0,
+ "proportion":0.1387433808480476
+ },
+ "2":{
+ "omega":1,
+ "proportion":0.8403256984411339
+ }
+ }
+ },
+ "display order":3,
+ "estimated parameters":39
+ },
+ "MG94xREV with separate rates for branch sets":{
+ "AIC-c":6997.089050462658,
+ "Equilibrium frequencies": [
+[0.04875339327772683],
+ [0.03982858547830345],
+ [0.04946803524790992],
+ [0.04152216138298744],
+ [0.01811683453600613],
+ [0.01480036248560469],
+ [0.0183823965708893],
+ [0.01542969784826435],
+ [0.01894694796506697],
+ [0.01547851515238824],
+ [0.01922467805342367],
+ [0.01613668666381816],
+ [0.02832099415740372],
+ [0.02313654621336914],
+ [0.02873613184734657],
+ [0.02412034959764736],
+ [0.01662182431200483],
+ [0.01357902918971745],
+ [0.01686547203528639],
+ [0.01415643148428886],
+ [0.006176695005242439],
+ [0.005045987744654046],
+ [0.006267234867003878],
+ [0.005260551308914496],
+ [0.006459711194459957],
+ [0.005277194922783805],
+ [0.006554399593040238],
+ [0.005501589790395056],
+ [0.009655668202293983],
+ [0.007888099278638223],
+ [0.009797203904398108],
+ [0.008223514024394991],
+ [0.03326722643528176],
+ [0.02717732003095303],
+ [0.03375486749252685],
+ [0.02833294365668738],
+ [0.01236215156074466],
+ [0.01009913314808799],
+ [0.01254335971371867],
+ [0.01052856463184265],
+ [0.01292858539344675],
+ [0.0105618754683007],
+ [0.0131180965046964],
+ [0.01101098350431497],
+ [0.0193250328267319],
+ [0.01578738770911659],
+ [0.0196083049972345],
+ [0.01645869298147252],
+ [0.01962343746171723],
+ [0.02045785777700414],
+ [0.008926115885166477],
+ [0.007292098982657142],
+ [0.009056957588961733],
+ [0.007602170831388156],
+ [0.007626222986467745],
+ [0.009471947420992787],
+ [0.007950502328516303],
+ [0.01395367801862353],
+ [0.01139931439306339],
+ [0.01415821524731906],
+ [0.01188403168729233]
+ ],
+ "Log Likelihood":-3467.004808147542,
+ "Rate Distributions":{
+ "non-synonymous/synonymous rate ratio for *test*": [
+[0.9950576192409499, 1]
+ ]
+ },
+ "display order":1,
+ "estimated parameters":31
+ },
+ "Nucleotide GTR":{
+ "AIC-c":7112.85745601076,
+ "Equilibrium frequencies": [
+[0.3592490842490842],
+ [0.181959706959707],
+ [0.240018315018315],
+ [0.2187728937728937]
+ ],
+ "Log Likelihood":-3532.321297387654,
+ "Rate Distributions":{
+ "Substitution rate from nucleotide A to nucleotide C":0.5497129763145497,
+ "Substitution rate from nucleotide A to nucleotide G":1,
+ "Substitution rate from nucleotide A to nucleotide T":0.264666902964203,
+ "Substitution rate from nucleotide C to nucleotide G":0.4916303643305098,
+ "Substitution rate from nucleotide C to nucleotide T":1.027924764411573,
+ "Substitution rate from nucleotide G to nucleotide T":0.304615404570875
+ },
+ "display order":0,
+ "estimated parameters":24
+ },
+ "Unconstrained model":{
+ "AIC-c":6910.766610587704,
+ "Log Likelihood":-3414.486640449675,
+ "Rate Distributions":{
+ "Synonymous site-to-site rates":{
+ "0":{
+ "proportion":0.2645541257391169,
+ "rate":0.2747941124675511
+ },
+ "1":{
+ "proportion":0.6325830460054784,
+ "rate":0.9734675888351726
+ },
+ "2":{
+ "proportion":0.1028628282554047,
+ "rate":3.028333913894314
+ }
+ },
+ "Test":{
+ "0":{
+ "omega":0,
+ "proportion":0.04809457608200497
+ },
+ "1":{
+ "omega":0,
+ "proportion":0.3410012743721951
+ },
+ "2":{
+ "omega":1.89363684081788,
+ "proportion":0.6109041495458
+ }
+ }
+ },
+ "display order":2,
+ "estimated parameters":40
+ }
+ },
+ "input":{
+ "file name":"/tmp/tmp7qHfo2/job_working_directory/000/3/working/./busted_input.fa",
+ "number of sequences":10,
+ "number of sites":187,
+ "partition count":1,
+ "trees":{
+ "0":"((((Pig:0.147969,Cow:0.21343)Node3:0.08509899999999999,Horse:0.165787,Cat:0.264806)Node2:0.058611,((RhMonkey:0.002015,Baboon:0.003108)Node9:0.022733,(Human:0.004349,Chimp:0.000799)Node12:0.011873)Node8:0.101856)Node1:0.340802,Rat:0.050958,Mouse:0.09795)"
+ }
+ },
"test results":{
- "LRT":44.77492170961614,
- "p-value":1.893429857346973e-10
+ "LRT":10.17362366082671,
+ "p-value":0.003088842014430382
+ },
+ "tested":{
+ "0":{
+ "Baboon":"test",
+ "Cat":"test",
+ "Chimp":"test",
+ "Cow":"test",
+ "Horse":"test",
+ "Human":"test",
+ "Mouse":"test",
+ "Node1":"test",
+ "Node12":"test",
+ "Node2":"test",
+ "Node3":"test",
+ "Node8":"test",
+ "Node9":"test",
+ "Pig":"test",
+ "Rat":"test",
+ "RhMonkey":"test"
+ }
+ },
+ "timers":{
+ "Constrained BUSTED model fitting":{
+ "order":3,
+ "timer":62
+ },
+ "Overall":{
+ "order":0,
+ "timer":228
+ },
+ "Preliminary model fitting":{
+ "order":1,
+ "timer":3
+ },
+ "Unconstrained BUSTED model fitting":{
+ "order":2,
+ "timer":161
+ }
}
}
\ No newline at end of file
diff -r 7b3f9c78cf6d -r d02c8e6f7f2a test-data/gard-out1.nex
--- a/test-data/gard-out1.nex Wed Aug 21 12:26:38 2019 -0400
+++ b/test-data/gard-out1.nex Thu Feb 13 15:03:27 2020 -0500
@@ -3,7 +3,7 @@
BEGIN TAXA;
DIMENSIONS NTAX = 21;
TAXLABELS
- 'TREESPARROW_HENAN_1_2004' 'HUMAN_VIETNAM_CL105_2005' 'TREESPARROW_HENAN_4_2004' 'CHICKEN_HEBEI_326_2005' 'CHICKEN_HONGKONG_915_97' 'VIETNAM_3062_2004' 'GOOSE_HONGKONG_W355_97' 'DUCK_HONGKONG_Y283_97' 'DUCK_VIETNAM_376_2005' 'MALLARD_VIETNAM_16_2003' 'CHICKEN_THAILAND_KANCHANABURI_CK_160_2005' 'DUCK_GUANGZHOU_20_2005' 'CK_HK_WF157_2003' 'SWINE_ANHUI_2004' 'DUCK_VIETNAM_272_2005' 'HONGKONG_97_98' 'GOOSE_SHANTOU_2216_2005' 'TREESPARROW_HENAN_3_2004' 'PEREGRINEFALCON_HK_D0028_2004' 'TREESPARROW_HENAN_2_2004' 'HONGKONG_538_97' ;
+ 'TREESPARROW_HENAN_1_2004' 'TREESPARROW_HENAN_3_2004' 'TREESPARROW_HENAN_4_2004' 'CHICKEN_HEBEI_326_2005' 'SWINE_ANHUI_2004' 'TREESPARROW_HENAN_2_2004' 'CHICKEN_HONGKONG_915_97' 'GOOSE_HONGKONG_W355_97' 'DUCK_HONGKONG_Y283_97' 'HONGKONG_97_98' 'HONGKONG_538_97' 'DUCK_GUANGZHOU_20_2005' 'GOOSE_SHANTOU_2216_2005' 'PEREGRINEFALCON_HK_D0028_2004' 'CK_HK_WF157_2003' 'HUMAN_VIETNAM_CL105_2005' 'DUCK_VIETNAM_376_2005' 'VIETNAM_3062_2004' 'MALLARD_VIETNAM_16_2003' 'CHICKEN_THAILAND_KANCHANABURI_CK_160_2005' 'DUCK_VIETNAM_272_2005' ;
END;
BEGIN CHARACTERS;
@@ -16,240 +16,35 @@
MATRIX
'TREESPARROW_HENAN_1_2004' ATGGAGAAAATAGTGCTTCTTCGTGCAATGATCAATCTTGTTAAAAGTGATCAGATTGGCGTTGGTTACCATGCAGACTACTCGACAGAGCAGGGTGACACAATAATGGAAAAGAACGTTACTGTTACACATGCTCAAGACATATTGGAAAAGACACACAACGGGAAGCTCTGCGACCTAGATGGAGTGAAGCCTCTAATTTTGAAAGATTGTAGTGTAGCTGGATGGCTCCTCGGAAACCCAATGTGTGACGAATTCATCAATGTGCCGGAGTGGTCTTACATAGTGGAGAAGGCCAGTCCAGCCAATGACCTCTGTTACCCAGGGGATTTCAACGACTATGAAGAACTGAAACACCTATTGAGCAGAATAAACCATTTTGAAAAAATTCAGATCATCCCCAAAAGTTCTTGGTCCGATCATGAAGCCTCATCAGGGGTGAGCTCAGCATGTCCATACCTGGGGAAGCCCTCCTTTTTCAGAAATGTGGTATGGCTTATCAAAAAGAACAGTACATACCCAACAATAAAGAGGGGCTACAATAATACCAACCCAGAAGATCTTTTGGTACTGTGGGGGATTCACCATCCTAATGATGCGGCAGAGCAGATAAAGCTCTATCAAAACCCAACCACCTATATTTCCGTTGGAACATCAACACTAAACCAGAGATTGGTACCAAAAATAGCTACTAGATCCAAAGTAAATGGGCAAAGTGGAAGAATGGAGTTCTTCTGGACAATTTTAAAGCCGAATGACGCTATCAACTTCGAGAGTAATGGAAATTTCATTGCTCCAGAATATGCATACCAAATTGTCAAGAAAGGGGACTCAGCAATTATGAAAAGTGAATTGGAATATGGTAACTGCAACACCAAGTGTCAAACTCCAATGGGGGCGATAAACTCTAGTATGCCATTCCACAACATACACCCTCTCACCATCGGGGAATGCCCCAAATATGTGAAATCAAACAGATTAGTCCTTGCGACAGGGCTCAGAAATAGCCCTCAAAGAGAGAGAAGAAGAAAAAAGAGAGGACTATTTGGAGCTATAGCAGGTTTTATAGAGGGAGGATGGCAGGGAATGGTAGATGGTTGGTATGGGTACCACCATAGCAATGAGCAGGGGAGTGGATACGCTGCAGACAAAGAATCCACTCAAAAAGCAATAGATGGAGTCACCAATAAGGTCAACTCGATCATTGACAAAATGAACACTCAGTTTGAGGCCGTTGGAAGGGAATTTAATAACTTAGAAAGGAGAATAGAAAATTTAAACAAGAAGATGGAGGACGGATTCCTAGATGTCTGGACTTATAATGCTGAACTTCTGGTTCTCATGGAAAATGAGAGAACTCTAGACTTTCATGACTCAAATGTCAAGAACCTTTACGAAAAGGTCCGACTACAACTTAGGGATAATGCAAAGGAGCTGGGTAACGGTTGTTTCGAGTTCTATCACAAATGTGATAATGAATGTATGGAAAGTGTAAAAAACGGAACGTATGACTACCCGCAGTATTCAGAAGAAGCAAGACTAAACAGAGAGGAAATAAGTGGAGTAAAATTGGAATCAATAGGAACTTACCAAATACTGTCAATTTATTCAACAGTGGCGAGTTCCCTAGCACTGGCAATCATGGTAGCTGGTCTATCTTTATGGATGTGCTCCAATGGATCGTTACAATGCAGAATT
- 'HUMAN_VIETNAM_CL105_2005' ATGGAGAAAATAGTGCTTCTTTTTGCGATAGTCAGTCTTGTTAAAAGTGATCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACACAATAATGGAAAAGAACGTTACTGTTACACATGCCCAAGACATACTGGAAAAGACACACAACGGGAAGCTCTGCGATCTAGATGGAGTGAAGCCTCTAATTTTGAGAGATTGTAGTGTAGCTGGATGGCTACTCGGAAACCCAATGTGTGACGAATTCATCAATGTGCCGGAATGGTCTTACATAGTGGAGAAGGTCAATCCAGTCAATGACCTCTGTTACCCAGGGGTTTTCAATGACTATGAAGAATTGAAACACCTATTGAGCAGAATAAACCATTTTGAGAAAATTCAGATCATCCCCAAAAGTTCTTGGTCCAGTCATGAAGCCTCATTAGGGGTGAGCTCAGTATGTCCATACCAGGGAAAGTCCTCCTTTTTCAGAAATGTGGTATGGCTTATCAAAAAGAACAGTACATACCCAACAATAAAGAGGAGCTACAATAATACCAACCAAGAAGATCTTTTGGTAATATGGGGGATTCATCATCCTAATGATGCGGCAGAGCAGATAAAGCTCTATCAAAACCCAACCACCTATATTTCCGTTGGGACATCAACACTAAACCAGAGATTGGTACCAAGAATAGCTACTAGATCCAAAGTAAACGGGCAAAGTGGGAGGATGGAGTTCTTCTGGACAATTTTAAAACCGAATGATGCAATCAACTTCGAGAGTAATGGAAATTTCATTGCTCCAGAATATGCATACAAGATTGTCAAGAAAGGGGACTCAACAATTATGAAAAGTGAATTGGAATATGGTAACTGCAACACCAAGTGTCAAACTCCAATGGGGGCGATAAACTCTAGTATGCCATTCCACAATATACACCCTCTCACCATCGGGGAATGCCCCAAATATGTGAAATCAAACAGATTAGTCCTTGCGACTGGGCTCAGAAATAGCCCTCAAAAAGAGAGAAGAAGAAAAAAGAGAGGATTATTTGGAGCTATAGCAGGTTTTATAGAGGGAGGATGGCAGGGAATGGTAGATGGTTGGTATGGGTACCACCATAGCAATGAGCAGGGGAGTGGGTACGCTGCAGACAAAGAATCCACTCAAAAGGCAATAGATGGAGTCACCAATAAGGTCAACTCGATCATTGACAAAATGAACACTCAGTTTGAGGCCGTTGGAAGGGAATTTAACAACTTAGAAAGGAGAATAGAGAATTTAAACAAGAAGATGGAAGACGGGTTCCTAGATGTCTGGACTTATAATGCTGAACTTCTGGTTCTCATGGAAAATGAGAGAACTCTAGACTTTCATGACTCAAATGTCAAGAACCTTTACGACAAGGTCCGACTACAGCTTAGGGATAATGCAAAGGAGCTGGGTAACGGTTGTTTCGAGTTCTATCATAAATGTGATAATGAATGTATGGAAAGTGTAAGAAACGGAACGTATGACTACCCGCAGTATTCAGAAGAAGCAAGATTAAAAAGAGAGGAAATAAGTGGAGTAAAATTGGAATCAATAGGAATTTACCAAATACTGTCAATTTATTCTACAGTGGCGAGTTCCCTAGCACTGGCAATCATGATAGCTGGTCTATCCTTATGGATGTGCTCCAATGGGTCGTTACAA---------
+ 'TREESPARROW_HENAN_3_2004' ATGGAGAAAATAGTGCTTCTTCTTGCAATAGTCAGTCTTGTTAAAAGTGATCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACACTATAATGGAAAAGAACGTTACTGTTACACATGCCCAAGACATACTGGAAAAGACACACAACGGGAAGCTCTGCGATCTAGATGGAGTGAAGCCTCTAATTTTGAGAGATTGTAGTGTAGCTGGATGGCTCCTCGGAAACCCAATGTGTGACGAATTCATCAATGTGCCGGAATGGTCTTACATAGTGGAGAAGGCCAGTCCAGCCAATGACCTCTGTTACCCAGGGGATTTCAACGACTATGAAGAACTGAAACACCTATTGAGCAGAATAAACCATTTTGAGAAAATTCGGATCATCCCCAAAAGTTCTTGGTCCAATCATGATGCCTCATCAGGGGTGAGCTCAGCATGTCCATACCAGGGGAAGCCCTCCTTTTTCAGAAATGTGGTATGGCTTATCAAAAAGAACAGTACATACCCAACGATAAAGAGGAGCTACAATAATACCAACCCAGAAGATCTTTTGGTACTGTGGGGGATTCACCATCCTAATGATGCGGCAGAGCAGATAAAGCTCTATCAAAACCCAACCACCTATATTTCCGTTGGAACATCAACACTAAACCAGAGATTGGTACCAAAAATAGCTACTAGATCCAAAGTAAATGGGCAAAGTGGAAGAATGGAGTTCTTCTGGACAATTTTAAAGCCGAATGACGCTATCAACTTCGAGAGTAATGGAAATTTCATTGCTCCAGAATATGCATACAAAATTGTCAAGAAAGGGGACTCAGCAATTATGAAAAGTGAATTGGAATATGGTAACTGCAACACCAAGTGTCAAACTCCAATGGGGGCGATAAATTCTAGTATGCCATTCCACAACATACACCCTCTCACCATCGGGGAATGCCCCAAATATGTGAAATCAAACAGATTAGTCCTTGCGACAGGGCTCAGAAATAGCCCTCAAAGAGAGGGAAGAAGAAAAAAGAGAGGACTATTTGGAGCTATAGCAGGTTTTATAGAGGGAGGATGGCAGGGAATGGTAGATGGTTGGTATGGGTACCACCATAGCAATGAGCAGGGGAGTGGATACGCTGCAGACAAAGAATCCACTCAAAAAGCAATAGATGGAGTCACCAATAAGGTCAACTCGATCATTGACAAAATGAACACTCAGTTTGAGGCCGTTGGAAGGGAATTTAATAACTTAGAAAGGAGAATAGAAAATTTAAACAAGAAGATGGAGGACGGATTCCTAGATGTCTGGACTTATAATGCTGAACTTCTGGTTCTCATGGAAAATGAGAGAACTCTAGACTTTCATGACTCAAATGTCAAGAACCTTTACGAAAAGGTCCGACTACAACTTAGGGATAATGCAAAGGAGCTGGGTAACGGTTGTTTCGAGTTCTATCACAAATGTGATAATGAATGTATGGAAAGTGTAAAAAACGGAACGTATGACTACCCGCAGTATACGGAAGAAGCAAGACTAAACAGAGAGGAAATAAGTGGAGTAAAATTGGAATCAATAGGAACTTACCAAATACTGTCAATTTATTCAACAGTAGTGAGTTCCCTAGCACTGGCAATCATGGTAGCTGGTCTATCTTTATGGATGTGCTCCAATGGATCGTTACAATGCAGAATT
'TREESPARROW_HENAN_4_2004' ATGGAGAAAATAGTGCTTCTTCTTGCAATAGTCAGTCTTGTTAAAAGTGATCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACACAATAATGCAAAAGAACGTTACTGTTACACATGCCCAAGACATACTGGAAAAGACACACAACGGGAAGCTCTGCGATCTAGATGGAGTGAAACCTCTAATTTTAAGAGATTGTAGTGTAGCTGGATGGCTCCTCGGAAACCCAATGTGTGACGAATTCATCAATGTGCCGGAATGGTCTTACATAGTGGAGAAGGCCAGTCCAGCCAATGACCTCTGTTACCCAGGGGATTTCAACGACTATGAAGAACTGAAACACCTATTGAGCAGAATAAACCATTTTGAGAAAATTCAGATCATCCCCAAAAGTTCTTGGTCCGATCATGAAGCCTCATCAGGGGTGAGCTCAGCATGTCCATACCAGGGGAGTCCCTCCTTTTTCAGAAATGTGGTATGGCTTATCAAAAAGAACAGTGCATACCCAACAATAAAGAGGAGCTACAATAATACCAACCAAGAAGATCTTTTGGTACTGTGGGGGATTCACCATCCTAATGATGCGGCAGAGCAGACAAAGCTCTATCAAAACCCAACCACCTATATTTCCGTTGGAACATCAACACTAAACCAGAGATTGGTACCAAAAATAGCTACTAGATCCAAAGTAAATGGGCAAAGTGGAAGAATGGAGTTCTTCTGGACAATTTTAAAGCCGAATGACGCTATCAACTTCGAGAGTAATGGAAATTTCATTGCTCCAGAATATGCATACAAAATTGTCAAGAAAGGGGACTCAGCAATTATGAAAAGTGAATTGGAATATGGTAACTGCAACACCAAGTGTCAAACTCCAATGGGGGCGATAAACTCTAGTATGCCATTCCACAACATACACCCTCTCACCATCGGGGAATGCCCCAAATATGTGAAATCAAACAGATTAGTCCTTGCGACAGGGCTCAGAAATAGCCCTCAAAGAGAGAGAAGAAGAAAAAAGAGAGGACTATTTGGAGCTATAGCAGGTTTTATAGAGGGAGGATGGCAGGGAATGGTAGATGGTTGGTATGGGTACCACCATAGCAATGAGCAGGGGAGTGGATACGCTGCAGACAAAGAATCCACTCAAAAGGCAATAGATGGAGTCACCAATAAGGTCAACTCGATCATTGACAAAATGAACACTCAGTTTGAGGCCGTTGGAAGGGAATTTAATAACTTAGAAAGGAGAATAGAAAATTTAAACAAGAAGATGGAGGACGGATTCCTAGATGTCTGGACTTATAATGCTGAACTTCTGGTTCTCATGGAAAATGAGAGAACTCTAGACTTTCATGACTCAAATGTCAAGAACCTTTACGAAAAGGTCCGACTACAACTTAGGGATAATGCAAAGGAGCTGGGTAACGGTTGTTTCGAGTTCTATCACAAATGTGATAATGAATGTATGGAAAGTGTAAAAAACGGAACGTATGACTACCCGCAGTATTCAGAAGAAGCAAGACTAAACAGAGAGGAAATAAGTGGAGTAAAATTGGAATCAATAGGAACTTACCAAATACTGTCAATTTATTCAACAGTGGTGAGTTCCCTAGCACTGGCAATCATGGTAGCTGGTCTATCTTTATGGATGTGCTCCAATGGATCGTTACAATGCAGAATT
'CHICKEN_HEBEI_326_2005' ATGGAGAGAATAGTGCTTCTTCTTGCAATAATCGGTCTTGTTAAAAGTGATCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACACAATAATGGAAAAGAACGTTACTGTTACACATGCTCAAGACATACTGGAGAAGACACACAACGGGAAGCTCTGCAACCCAGATGGAGTGAAGCCTCTAATTTTGAAAGATTGTAGTGTAGCTGGATGGCTCCTCGGAAACCCAATGTGTGACGAATTTATCAATGTGCCGGAATGGTCTTACATAGTGGAGAAGGCCAGTCCAGCCAATGGCCTCTGTTACCCAGGGGATTTCAATGACTATGAAGAACTGAAACACCTATTGAGCAGAATAAACCATTTTGAGAAAATTCAGATCATCCCCAAAAGTTCTTGGTCCGATCATGGAGCCTCATCAGGGGTGAGCTCAGCATGTTCCTATCTGGGGAAGCCCTCCTTTTTCAGAAATGTGGTATGGCTTATCAAAAAGAATAATACATACCCACCAATAAAGGTGAGCTACAACAATACCAACCAAGAAGATCTTTTGGTACTGTGGGGGATTCACCATCCCAATGATGAGGCAGAGCAGATAAAGATCTATCAAAACCCAACCACCTATATTTCCGTTGGAACATCAACACTAAACCAGAGATTGGTACCAAAAATAGCTACTAGATCCAAAGTAAACGGGCAAAGTGGAAGAATGGAGTTCTTCTGGACAATTTTAAAGCCGAATGATGCTATCAATTTCGATAGTAATGGAAATTTCATTGCTCCAGAATATGCATACAAAATTGTCAAGAAAGGGGACTCAGCGATTATGAAAAGTGAATTGGAATATGGCAACTGCAACACCAAGTGTCAAACTCCAATGGGGGCGATAAATTCTAGTATGCCATTCCACAACATACACCCTCTCACCGTCGGGGAATGCCCCAAATATGTGAAATCAAACAGATTAGTCCTCGCGACTGGACTCAGAAATGCCCCTCAAAGAGAGGGAGGAAGAAAAAAGAGAGGACTATTTGGAGCCATAGCAGGGTTTATAGAGGGAGGATGGCAGGGAATGGTAGATGGTTGGTATGGGTACCACCATAGCAATGAGCAGGGGAGTGGATACGCTGCAGACAAAGAATCCACTCAAAAGGCAATAGATGGAGTCACCAATAAGGTCAACTCGATCATTGACAAAATGAACACTCAGTTTGAGGCCGTTGGAAGGGAATTTAATAACTTAGAAAGGAGAATAGAAAATTTAAACAAGAAGATGGAGGACGGATTCCTAGATGTCTGGACTTATAACGCTGAACTTCTGGTTCTCATGGAAAATGAGAGAACTCTAGACTTTCATGACTCAAATGTCAAGAACCTTTACGAAAAGGTCCGACTACAGCTTAGGGATAATGCAAAGGAGCTGGGTAACGGTTGTTTCGAGTTCTATCACAAATGTGATAATGAATGTATGGAAAGTGTAAAAAACGGAACGTATGACTACCCGCAGTATTCAGAAGAAGCAAGACTAAACAGAGAGGAAATAAGTGGAGTAAAATTGGAATCAATGGGAACTTACCAAATACTGTCAATTTATTCAACAGTGGCGAGTTCCCTAGCATTGGCAATCATGGTAGCTGGTCTATCTTTATGGATGTGCTCCAATGGATCGTTACAATGCAGAATT
+ 'SWINE_ANHUI_2004' ATGGAGAAAATAGTGCTTCTTCTTGCAATAGTCAGTCTTGTTAAAGGTGATCAGATTTGCACTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACACAATAATGGAAAAGAACGTTACTGTTACACATGCTCAAGACATACTGGAAAAGACACACAACGGGAAGCTCTGCGACCTAGATGGAGTGAAGCCTCTAATTTTAAGAGATTGTAGTGTAGCTGGATGGCTCCTCGGGAACCCAATGTGTGACGAATTCATCAATGTGCCGGAATGGTCTTACATAGTGGAGAAGGCCAATCCAGCCAATGACCTCTGTTACCCAGGGGATTTCAACGACTATGAAGAACTGAAACACCTATTGAGCAGAATAAACCATTTTGAGAAAATTCAGATCATCCCCAAAAGTTCTTGGTCCGATCATGAAGCCTCATCAGGGGTGAGCTCAGCATGTCCATACCAGGGAAGGTCCTCCTTTTTCAGAAATGTGGTATGGCTTATCAAAAAGAACAGTGCATACCCAACAATAAAGAGGAGCTACAATAATACCAACCAAGAAGATCTTTTGGTACTGTGGGGGATTCACCACCCTAATGATGCGGCAGAGCAGATAAAGCTCTATCAAAACCCAACCACCTATATTTCCGTTGGGACATCAACACTAAACCAGAGATTGGTACCAAAAATAGCTACTAGATCCAAAGTAAACGGACAAAGTGGAAGAATGGAGTTCTTCTGGACAATTTTAAAACCGAATGATGCTATCAATTTCGAGAGTAATGGAAATTTCATTGCTCCAGAATATGCATACAAAATTGTCAAGAAAGGGGACTCTGCAATTATGAAAAGTGAATTGGAATATGGCAACTGCAACACCAAGTGTCAAACTCCAGTGGGGGCGATAAATTCTAGCATGCCATTCCACAACATACACCCTCTCACCATCGGGGAATGCCCCAAATATGTGAAATCAAACAGATTAGTCCTTGCGACTGGACTCAGAAATGCCCCTCAAAGAGAGGGAAGAAGAAAAAAGAGAGGACTATTTGGAGCTATAGCAGGGTTTATAGAGGGAGGATGGCAGGGGATGGTAGATGGTTGGTATGGGTACCACCATAGCAATGAGCAGGGGAGTGGATACGCTGCAGACAAAGAATCCACTCAAAAAGCAATAGATGGAGTCACCAATAAGGTCAACTCGATCATTGACAAAATGAACACTCAGTTTGAGGCCGTTGGAAGGGAATTTAATAACTTAGAAAGGAGAATAGAAAATTTAAACAAGAAGATGGAGGACGGATTCCTAGATGTCTGGACTTATAATGCTGAACTTCTGGTTCTCATGGAAAATGAGAGAACTCTAGACTTTCATGACTCAAATGTCAAGAACCTTTACGACAAGGTCCGACTACAGCTTAGGGATAATGCAAAGGAGCTGGGTAACGGTTGTTTCGAGTTCTATCACAGATGTGATAATGAATGTATGGAAAGTGTAAGAAACGGAACGTATGACTACCCGCAGTATTCGGAAGAAGCAAGACTAAACAGAGAGGAAATAAGTGGAGTAAAATTGGAATCAATAGGAACTTACCAAATACTGTCAATTTATTCAACAGTGGCGAGTTCCCTAGCACTGGCAATCATGGTGGCTGGTCTATCTTTATGGATGTGCTCCAATGGATCGTTACAATGCAGAATT
+ 'TREESPARROW_HENAN_2_2004' ATGGAGAAAATAGTGCTTCTTCTTGCAATAGTCAGTCTTGTTAAAAGTGATCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACACAATAATGGAAAAGAACGTTACTGTTACACATGCTCAAGACATATTGGAAAAGACACACAACGGGAAGCTCTGCGACCTAGATGGAGTGAAGCCTCTAATTTTGAAAGATTGTAGTGTAGCTGGATGGCTCCTCGGAAACCCAATGTGTGACGAATTCATCAATGTGCCGGAGTGGTCTTACATAGTGGAGAAGGCCAGTCCAGCCAATGACCTCTGTTACCCAGGGGATTTCAACGACTATGAAGAACTGAAACACCTATTGAGCAGAATAAACCATTTTGAAAAAATTCAGATCATCCCCAAAAGTTCTTGGTCCGATCATGAAGCCTCATCAGGGGTGAGCTCAGCATGTCCATACCTGGGGAAGCCCTCCTTTTTCAGAAATGTGGTATGGCTTATCAAAAAGAACAGTACATACCCAACAATAAAGAGGGGCTACAATAATACCAACCAAGAAGATCTTTTGGTACTGTGGGGGATTCACCATCCTAATGATGCGGCAGAGCAGATAAAGCTCTATCAAAACCCAACCACCTATATTTCCGTTGGAACATCAACACTAAACCAGAGATTGGTACCAAAAATAGCTACTAGATCCAAAGTAAACGGACAAAGTGGAAGAATGGAGTTCTTCTGGACAATTTTAAAACCGAATGATGCTATCAATTTCGAGAGTAATGGAAATTTCATTGCTCCAGAATATGCATACAAAATTGTCAAGAAAGGGGACTCTGCAATTATGAAGAGTGAATTGGAATATGGCAACTGCAACACCAAGTGTCAAACTCCAGTGGGGGCGATAAATTCTAGCATGCCATTCCACAACATACACCCTCTCACCATCGGGGAATGCCCCAAATATGTGAAATCAAACAGATTAGTCCTTGCGACTGGACTCAGAAATGCCCCTCAAAGAGAGGGAAGAAGAAAAAAGAGAGGACTATTTGGAGCTATAGCAGGGTTTATAGAGGGAGGATGGCAGGGGATGGTAGATGGTTGGTATGGGTACCACCATAGCAATGAGCAGGGGAGTGGATACGCTGCAGACAAAGAATCCACTCAAAAAGCAATAGATGGAGTCACCAATAAGGTCAACTCGATCATTGACAAAATGAACACTCAGTTTGAGGCCGTTGGAAGGGAATTTAATAACTTAGAAAGGAGAATAGAAAATTTAAACAAGAAGATGGAGGACGGATTCCTAGATGTCTGGACTTATAATGCTGAACTTCTGGTTCTCATGGAAAATGAGAGAACTCTAGACTTTCATGACTCAAATGTCAAGAACCTTTACGAAAAGGTCCGACTACAACTTAGGGATAATGCAAAGGAGCTGGGTAACGGTTGTTTCGAGTTCTATCACAAATGTGATAATGAATGTATGGAAAGTGTAAAAAACGGAACGTATGACTACCGGCTGGACTCAGAAGAAGCAAGACTAAACAGAGAGGAAATAAGTGGAGTAAAATTGGAATCAATAGGAACTTACCAAATACTGTCAATTTATTCAACAGTGGCGAGTTCCCTAGCACTGGCAATCATGGTAGCTGGTCTATCTTTATGGATGTGCTCCAATGGATCGTTACAATGCAGAATT
'CHICKEN_HONGKONG_915_97' ATGGAGAAAATAGTGCTTCTTCTTGCAACAGTCAGTCTTGTTAAAAGTGATCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACACAATAATGGAAAAGAATGTTACTGTTACACATGCCCAAGACATACTGGAAAGGACACACAACGGGAAGCTCTGCGATCTAAATGGAGTGAAACCTCTCATTTTGAGGGATTGTAGTGTAGCTGGATGGCTCCTCGGAAACCCTATGTGTGACGAATTCATCAATGTGCCGGAATGGTCTTACATAGTGGAGAAGGCCAGTCCAGCCAATGACCTCTGTTATCCAGGGAATTTCAACGACTATGAAGAACTGAAACACCTATTGAGCAGAATAAACCATTTTGAGAAAATTCAGATCATCCCCAAAAGTTCTTGGTCCAATCATGATGCCTCATCAGGGGTGAGCTCAGCATGTCCATACCTTGGGAGGTCCTCCTTTTTCAGAAATGTGGTATGGCTTATCAAAAAGAACAGTGCATACCCAACAATAAAGAGGAGCTACAATAATACCAACCAAGAAGATCTTTTGGTACTGTGGGGGATTCACCATCCTAATGATGCGGCAGAGCAGACAAAGCTCTATCAAAATCCAACCACCTACATTTCCGTTGGAACATCAACACTGAACCAGAGATTGGTTCCAGAAATAGCTACTAGACCCAAAGTAAACGGGCAAAGTGGAAGAATGGAGTTCTTCTGGACAATTTTAAAGCCGAATGATGCCATCAATTTCGAGAGTAATGGAAATTTCATTGCCCCAGAATATGCATACAAAATTGTCAAGAAAGGGGACTCAACAATTATGAAAAGTGAATTGGAATATGGTAACTGCAACACCAAGTGTCAAACTCCAATGGGGGCGATAAACTCTAGTATGCCATTCCACAACATACACCCCCTCACCATCGGGGAATGCCCCAAATATGTGAAATCAAACAGATTAGTTCTTGCGACTGGACTCAGAAATACCCCTCAAAGGGAGAGAAGAAGAAAAAAGAGAGGACTATTTGGAGCTATAGCAGGTTTTATAGAGGGAGGATGGCAGGGCATGGTAGATGGTTGGTATGGGTACCACCATAGCAATGAGCAGGGGAGTGGATACGCTGCAGACAAAGAATCCACTCAAAAGGCAATAGATGGAGTCACCAATAAGGTCAACTCGATCATTAACAAAATGAACACTCAGTTTGAGGCCGTTGGAAGGGAATTTAATAACTTAGAAAGGAGAATAGAGAATTTAAACAAGAAAATGGAAGACGGATTCCTAGATGTCTGGACTTACAATGCTGAACTTCTGGTTCTCATGGAAAATGAGAGAACTCTCGACTTTCATGACTCAAATGTCAAGAACCTTTACGACAAGGTCCGACTACAGCTTAGGGATAATGCAAAGGAACTGGGTAATGGTTGTTTCGAATTCTATCACAAATGTGATAATGAATGTATGGAAAGTGTAAAAAACGGAACGTATGACTACCCGCAGTATTCAGAAGAAGCAAGACTAAACAGAGAGGAAATAAGTGGAGTAAAATTGGAATCAATGGGAACTTACCAAATACTGTCAATTTATTCAACAGTGGCGAGTTCCCTAGCACTGGCAATCATGGTAGCTGGTCTATCTTTATGGATGTGCTCCAATGGATCGTTACAATGCAGAATT
- 'VIETNAM_3062_2004' ATGGAGAAAATAGTGCTTCTTTTTGCAATAGTCAGTCTTGTTAAAAGTGATCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACACAATAATGGAAAAGAACGTTACTGTTACACATGCCCAAGACATACTGGAAAAGACACACAACGGGAAGCTCTGCGATCTAGATGGAGTGAAGCCTCTAATTTTGAGAGATTGTAGTGTAGCTGGATGGCTCCTCGGAAACCCAATGTGTGACGAATTCATCAATGTGCCGGAATGGTCTTACATAGTGGAGAAGGCCAATCCAGTCAATGACCTCTGTTACCCAGGGGATTTCAATGACTATGAAGAATTGAAACACCTATTGAGCAGAATAAACCATTTTGAGAAAATTCAGATCATCCCCAAAAGTTCTTGGTCCAGTCATGAAGCCTCATTAGGAGTGAGCTCAGCATGTCCATACCAGGGAAAGTCCTCCTTTTTCAGAAATGTGGTATGGCTTATCAAAAAGAACAGTACATACCCAACAATAAAGAGGAGCTACAATAATACCAACCAAGAAGATCTTTTGGTACTGTGGGGGATTCACCATCCTAATGATGCGGCAGAGCAGACAAAGCTCTATCAAAACCCAACCACCTATATTTCCGTTGGGACATCAACACTAAACCAGAGGTTGGTACCAAGAATAGCTACTAGATCCAAAGTAAACGGGCAAAGTGGAAGGATGGAGTTCTTCTGGACAATTTTAAAACCGAATGATGCAATCAACTTCGAGAGTAATGGAAATTTCATTGCTCCAGAATATGCATACAAAATTGTCAAGAAAGGGGACTCAACAATTATGAAAAGTGAATTGGAATATGGTAACTGCAACACCAAGTGTCAAACTCCAATGGGGGCGATAAACTCTAGTATGCCATTCCACAATATACACCCTCTCACCATCGGGGAATGCCCCAAATATGTGAAATCAAACAGATTAGTCCTTGCGACTGGGCTCAGAAATAGCCCTCAAAGAGAGAGAAGAAGAAAAAAGAGAGGATTATTTGGAGCTATAGCAGGTTTTATAGAGGGAGGATGGCAGGGAATGGTAGATGGTTGGTATGGGTACCACCATAGCAATGAGCAGGGGAGTGGGTACGCTGCAGACAAAGAATCCACTCAAAAGGCAATAGATGGAGTCACCAATAAGGTCAACTCGATCATTGACAAAATGAACACTCAATTTGAGGCCGTTGGAAGGGAATTTAACAACTTAGAAAGGAGAATAGAGAATTTAAACAAGAAGATGGAAGACGGGTTCCTAGATGTCTGGACTTATAATGCTGAACTTCTGGTTCTCATGGAAAATGAGAGAACTCTAGACTTTCATGACTCAAATGTCAAGAACCTTTACGACAAGGTCCGACTACAGCTTAGGGATAATGCAAAGGAGCTGGGTAACGGTTGTTTCGAGTTCTATCATAAATGTGATAATGAATGTATGGAAAGTGTAAGAAACGGAACGTATGACTACCCGCAGTATTCAGAAGAAGCAAGACTAAAAAGAGAGGAAATAAGTGGAGTAAAATTGGAATCAATAGGAATTTACCAAATACTGTCAATTTATTCTACAGTGGCGAGTTCCCTAGCACTGGCAATCATGGTAGCTGGTCTATCCTTATGGATGTGCTCCAATGGGTCG---------------
'GOOSE_HONGKONG_W355_97' ATGGAGAAAATAGTGCTTCTTCTTGCAACAGTCAGTCTTGTTAAAAGTGATCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACACAATAATGGAAAAGAATGTTACTGTTACACATGCCCAAGACATACTGGAAAGGACACACAACGGGAAGCTCTGCGATCTAAATGGAGTGAAACCTCTCATTTTGAGGGATTGTAGTGTAGCTGGATGGCTCCTCGGAAACCCTATGTGTGACGAATTCATCAATGTGCCGGAATGGTCTTACATAGTGGAGAAGGCCAGTCCAGCCAATGACCTCTGTTATCCAGGGAATTTCAACGACTATGAAGAACTGAAACACCTATTGAGCAGAATAAACCATTTTGAGAAAATTCAGATCATCCCCAAAAGTTCTTGGTCCAATCATGATGCCTCATCAGGGGTTAGCTCAGCATGTCCATACCTTGGGAGGTCCTCCTTTTTCAGAAATGTGGTATGGCTTATCAAAAAGAACAGTGCATACCCAACAATAAAGAGGAGCTACAATAATACCAACCAAGAAGATCTTTTGGTACTGTGGGGGATTCACCATCCTAATGATGCGGCAGAGCAGACAAAGCTTTATCAAAATCCAACCACCTACATTTCCGTTGGAACATCAACACTGAACCAGAGATTGGTTCCAGAAATAGCTACTAGACCCAAAGTAAACGGGCAAAGTGGAAGAATGGAGTTCTTCTGGACAATTTTAAAGCCGAATGATGCCATCAATTTCGAGAGTAATGGAAATTTCATTGCCCCAGAATATGCATACAAAATTGTCAAGAAAGGGGACTCAACAATTATGAAAAGTGAATTGGAATATGGTAACTGCAACACCAAGTGTCAAACTCCAATGGGGGCGATAAACTCTAGTATGCCATTCCACAACATACACCCCCTCACCATCGGGGAATGCCCCAAATATGTGAAATCAAACAGATTAGTTCTTGCGACTGGACTCAGAAATACCCCTCAAAGGGAGAGAAGAAGAAAAAAGAGAGGACTATTTGGAGCTATAGCAGGTTTTATAGAGGGAGGATGGCAGGGCATGGTAGATGGTTGGTATGGGTACCACCATAGCAATGAGCAGGGGAGTGGATACGCTGCAGACAAAGAATCCACTCAAAAGGCAATAGATGGAGTCACCAATAAGGTCAACTCGATCATTAACAAAATGAACACTCAGTTTGAGGCCGTTGGAAGGGAATTTAATAACTTAGAAAGGAGAATAGAGAATTTAAACAAGAAAATGGAAGACGGATTCCTAGATGTCTGGACTTACAATGCTGAACTTCTGGTTCTCATGGAAAATGAGAGAACTCTCGACTTTCATGACTCAAATGTCAAGAACCTTTACGACAAGGTCCGACTACAGCTTAGGGATAATGCAAAGGAACTGGGTAATGGTTGTTTCGAATTCTATCACAAATGTGATAATGAATGTATGGAAAGTGTAAGAAACGGAACGTATGACTACCCGCAGTATTCAGAAGAAGCAAGACTAAACAGAGAGGAAATAAGTGGAGTAAAATTGGAATCAATGGGAACTTACCAAATACTGTCAATTTATTCAACAGTGGCGAGTTCCCTAGCACTGGCAATCATGGTAGCTGGTCTATCTTTATGGATGTGCTCCAATGGATCGTTACAATGCAGAATT
'DUCK_HONGKONG_Y283_97' ATGGAGAAAATAGTGCTTCTTCTTGCAACAGTCAGTCTTGTTAAAAGTGATCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACACAATAATGGAAAAGAATGTTACTGTTACACATGCCCAAGACATACTGGAAAGGACACACAACGGGAAGCTCTGCGATCTAAATGGAGTGAAACCTCTCATTTTGAGGGATTGTAGTGTAGCTGGATGGCTCCTCGGAAACCCTATGTGTGACGAATTCATCAATGTGCCGGAATGGTCTTACATAGTGGAGAAGGCCAGTCCAGCCAATGACCTCTGTTATCCAGGGAATTTCAACGACTATGAAGAACTGAAACACCTATTGAGCAGAATAAACCATTTTGAGAAAATTCAGATCATCCCCAAAAGTTCTTGGTCCAATCATGATGCCTCATCAGGGGTTAGCTCAGCATGTCCATACCTTGGGAGGTCCTCCTTTTTCAGAAATGTGGTATGGCTTATCAAAAAGAACAGTGCATACCCAACAATAAAGAGGAGCTACAATAATACCAACCAAGAAGATCTTTTGGTACTGTGGGGGATTCACCATCCTAATGATGCGGCAGAGCAGACAAAGCTTTATCAAAATCCAACCACCTACATTTCCGTTGGAACATCAACACTGAACCAGAGATTGGTTCCAGAAATAGCTACTAGACCCAAAGTAAACGGGCAAAGTGGAAGAATGGAGTTCTTCTGGACAATTTTAAAGCCGAATGATGCCATCAATTTCGAGAGTAATGGAAATTTCATTGCCCCAGAATATGCATACAAAATTGTCAAGAAAGGGGACTCAACAATTATGAAAAGTGAATTGGAATATGGTAACTGCAACACCAAGTGTCAAACTCCAATGGGGGCGATAAACTCTAGTATGCCATTCCACAACATACACCCCCTCACCATCGGGGAATGCCCCAAATATGTGAAATCAAACAGATTAGTTCTTGCGACTGGACTCAGAAATACCCCTCAAAGGGAGAGAAGAAGAAAAAAGAGAGGACTATTTGGAGCTATAGCAGGTTTTATAGAGGGAGGATGGCAG---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+ 'HONGKONG_97_98' ------------------------------------------------GACCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGATACAATAATGGAAAAGAATGTTACTGTTACACATGCCCAAGACATACTGGAAAGGACACACGACGGGAAGCTCTGCGATCTAAATGGAGTGAAACCTCTCATTTTGAGGGATTGTAGTGTAGCTGGATGGCTCCTCGGAAACCCTATGTGTGACGAATTCATCAATGTGCCGGAATGGTCTTACATAGTGGAGAAGGCCAGTCCAGCCAATGACCTCTGTTATCCAGGGAATTTCAACGACTATGAAGAACTGAAACACCTATTGAGCAGAATAAACCATTTTGAGAAAATTCAGATCATCCCCAAAAGTTCTTGGTCCAATCATGATGCCTCATCAGGGGTGAGCTCAGCATGTCCATACCTTGGGAGGTCCTCCTTTTTCAGAAATGTGGTATGGCTTATCAAAAAGAACAGTGCATACCCAACAATAAAGAGGAGCTACAATAATACCAACCAAGAAGATCTTTTGGTACTGTGGGGGATTCACCATCCTAATGATGCGGCAGAGCAGACAAAGCTCTATCAAAATCCAACCACCTACATTTCCGTTGGAACATCAACACTGAATCAGAGATTGGTTCCAGAAATAGCTACTAGACCCAAAGTAAACGGGCAAAGTGGAAGAATGGAGTTCTTCTGGACAATTTTAAAGCCGAATGATGCCATCAATTTCGAGAGTAATGGAAATTTCATTGCCCCAGAATATGCATACAAAATTGTCAAGAAAGGGGACTCAACAATTATGAAAAGTGAATTGGAATATGGTAACTGCAACACCAAGTGTCAAACTCCAATGGGGGCGATAAACTCTAGTATGCCATTCCACAACATACACCCCCTCACCATCGGGGAATGCCCCAAATATGTGAAATCAAACAGATTAGTTCTTGCGACTGGACTCAGAAATACCCCTCATAGGGAGAGAAGAAGAAAAAAGAGAGGACTATTTGGAGCTATAGCAGGTTTTATAGAAGGAGGATGGCAGGGAATGGTAGATGGTTGGTATGGGTACCACCATAGCAATGAGCAGGGGAGTGGATACGCTGCAGACCAAGAATCCACTCAAAAGGCAATAGATGGAGTCACCAATAAGGTCAACTCGATCATTAACAAAATGAACACTCAGTTTGAGGCCGTTGGAAGGGAATTTAATAACTTAGAAAGGAGAATAGAGAATTTAAACAAGAAAATGGAAGACGGATTCCTAGATGTCTGGACTTACAATGCTGAACTTCTGGTTCTCATGGAAAATGAGAGAACTCTCGACTTTCATGACTCAAATGTCAAGAACCTTTACGACAAGGTCCGACTACAGCTTAGGGATAATGCAAAGGAACTGGGTAATGGTTGTTTCGAATTCTATCACAAATGTGATAATGAATGTATGGAAAGTGTAAAAAACGGAACGTATGACTACCCGCAGTATTCAGAAGAAGCAAGACTAAACAGAGAGGAAATAAGTGGAGTAAAATTGGAATCAATGGGAACTTACCAAATACTGTCAATTTATTCAACAGTGGCGAGTTCCCTAGCACTGGCAATCATGGTAGCTGGTCTATCTTTATGGATGTGCTCCAATGGATCGTTACAATGCAGAATT
+ 'HONGKONG_538_97' ------------------------------------------------GATCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACACAATAATGGAAAAGAATGTTACTGTTACACATGCCCAAGACATACTGGAAAGGACACACAACGGGAAGCTCTGCGATCTAAATGGAGTGAAACCTCTCATTTTGAGGGATTGTAGTGTAGCTGGATGGCTCCTCGGAAACCCTATGTGTGACGAATTCATCAATGTGCCGGAATGGTCTTACATAGTGGAGAAGGCCAGTCCAGCCAATGACCTCTGTTATCCAGGGAATTTCAACGACTATGAAGAACTGAAACACCTATTGAGCAGAATAAACCATTTTGAGAAAATTCAGATCATCCCCAAAAGTTCTTGGTCCAATCATGATGCCTCATCAGGGGTGAGCTCAGCATGTCCATACCTTGGGAGGTCCTCCTTTTTCAGAAATGTGGTATGGCTTATCAAAAAGAACAGTGCATACCCAACAATAAAGAGGAGCTACAATAATACCAACCAAGAAGATCTTTTGGTACTGTGGGGGATTCACCATCCTAATGATGCGGCAGAGCAGACAAAGCTCTATCAAAATCCAACCACCTACATTTCCGTTGGAACATCAACACTGAACCAGAGATTGGTTCCAGAAATAGCTACTAGACCCAAAGTAAACGGGCAAAGTGGAAGAATGGAGTTCTTCTGGACAATTTTAAAGCCGAATGATGCCATCAATTTCGAGAGTAATGGAAATTTCATTGCCCCAGAATATGCATACAAAATTGTCAAGAAAGGGGACTCAACAATTATGAAAAGTGAATTGGAATATGGTAACTGCAACACCAAGTGTCAAACTCCAATGGGGGCGATAAACTCTAGTATGCCATTCCACAACATACACCCCCTCACCATCGGGGAATGCCCCAAATATGTGAAATCAAACAGATTAGTTCTTGCGACTGGACTCAGAAATACCCCTCAAAGGGAGAGAAGAAGAAAAAAGAGAGGACTATTTGGAGCTATAGCAGGTTTTATAGAGGGAGGATGGCAGGGAATGGTAGATGGTTGGTATGGGTACCACCATAGCAATGAGCAGGGGAGTGGATACGCTGCAGACCAAGAATCCACTCAAAAGGCAATAGATGGAGTCACCAATAAGGTCAACTCGATCATTAACAAAATGAACACTCAGTTTGAGGCCGTTGGAAGGGAATTTAATAACTTAGAAAGGAGAATAGAGAATTTAAACAAGAAAATGGAAGACGGATTCCTAGATGTCTGGACTTACAATGCTGAACTTCTGGTTCTCATGGAAAATGAGAGAACTCTCGACTTTCATGACTCAAATGTCAAGAACCTTTACGACAAGGTCCGACTACAGCTTAGGGATAATGCAAAGGAACTGGGTAATGGTTGTTTCGAATTCTATCACAAATGTGATAATGAATGTATGGAAAGTGTAAGAAACGGAACGTATGACTACCCGCAGTATTCAGAAGAAGCAAGACTAAACAGAGAGGAAATAAGTGGAGTAAAATTGGAATCAATGGGAACTTACCAAATACTGTCAATTTATTCAACAGTGGCGAGTTCCCTAGCACTGGCAATCATGGTAGCTGGTCTATCTTTATGGATGTGCTCCAATGGATCGTTACAATGCAGAATT
+ 'DUCK_GUANGZHOU_20_2005' ATGGAGAAAATAGTGCTTCTTCTTGCAATAGTCAGTCTTGTTAAAAGTGATCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACACAATAATGGAAAAGAACGTTACTGTTACACATGCCCAAGACATACTGGAAAAGACACACAATGGGAAGCTCTGCGACCTAGATGGGGTGAAGCCTCTAATTTTGAGAGATTGTAGTGTAGCTGGATGGCTCCTCGGGAACCCAATGTGTGACGAATTCATCAATGTACCGGAATGGTCTTACATAGTGGAGAAGGCCAATCCAGCCAATGACCTCTGTTACCCAGGTGATTTCAACGATTATGAAGAACTGAAACACCTATTGAGCAGAATAAACCATTTTGAGAAAATTCAGATCATCCCCAAAAGTTCTTGGTCCAACCATGAATCCTCATCAGGGGTGAGCTCAGCATGTCCATACCTGGGAAAGCCCTCCTTTTTCAGAAATGTGGTATGGCTTATCAAAAAGAACAATGCATACCCAACAATAAAGAAGAGCTACAATAATACCAACCAAGAAGATCTTTTGGTACTGTGGGGGATTCACCATCCTAATGATGCGACAGAGCAGACAAAGCTCTATCAAAACCCAACCACTTATATTTCCGTTGGAACATCAACACTAAACCAGAGATTGGTACCAAAAATAGCTACCAGATCCAAAGTAAACGGGCAAAGTGGAAGGATGGAGTTCTTCTGGACAATTTTAAAACCGAATGATGCAATCAACTTCGAGAGTAATGGAAATTTCATTGCTCCAGAATATGCATACAAAATTGTCAAGAAAGGGGACTCAGCAATTATGAAAAGTGAATTGGAATATGGTAACTGCAACACCAAATGTCAAACTCCAATGGGGGCGATAAACTCTAGTATGCCATTCCACAACATACACCCTCTCACCATCGGGGAATGCCCCAAATATGTGAAATCAAACAGATTAGTCCTTGCGACTGGGCTCAGAAATAGCCCTCAAAGGGAGAGAAGAAGAAAGAAGAGAGGACTATTTGGAGCTATAGCAGGTTTTATAGAGGGAGGATGGCAGGGAATGGTAGATGGTTGGTATGGATACCACCATAGCAATGAGCAGGGGAGTGGATACGCTGCAGACAAAGAATCCACTCAAAAGGCAATAGATGGAGTCACCAATAAGGTCAACTCGATCATTGACAAAATGAACACTCAGTTTGAGGCCGTTGGAAGGGAATTTAATAACTTAGAAAGGAGAATAGAGAATTTAAACAAGAAGATGGAAGACGGATTCCTAGATGTCTGGACTTATAATGCTGAACTTCTGGTTCTCATGGAAAATGAGAGAACTCTAGACTTTCATGACTCAAATGTCAGGAACCTTTACGACAAGGTCCGACTACAGCTTAGGGATAATGCAAAAGAGCTGGGTAACGGTTGTTTCGAGTTCTATCACAAATGTGATGATGAATGCATGGAAAGTGTAAGAAACGGAACGTATGACTACCCGCAGTATTCAGAAGAAGCAAGGCTAAAAAGAGAGGAAATAAGTGGAGTAAAATTGGAATCAATAGGAACTTACCAAATACTGTCAATTTATTCAACAGTGGCAAGTTCCCTAGCGCTGGCAATCATGGTAGCTGGTCTATCTTTATGGATGTGCTCCAATGGTTCGTTACAATGCAGAATT
+ 'GOOSE_SHANTOU_2216_2005' ATGGAGAAAATAGTGCTTCTTCTTGCAATAATCAGCCTTGTTAAAAGTGATCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACACAATAATGGAAAAGAACGTTACTGTTACACATGCCCAAGACATACTGGAAAAGACACACAATGGGAAGCTCTGCGACTTAGATGGGGTGAAGCCTCTAATTTTGAGAGACTGTAGTGTAGCTGGATGGCTCCTCGGGAACCCAATGTGTGACGAATTCATCAATGTACCGGAATGGTCTTACATAGTGGAGAAGGCCAGTCCAGCCAATGACCTCTGTTACCCAGGTGATTTCAACGATTATGAAGAACTGAAACACCTATTGAGCAGAATAAACCATTTTGAGAAAATTCAGATCATCCCCAAAAGTTCTTGGTCCAATCATGAAGCCTCATCAGGGGTGAGCTCAGCATGTCCATACCTGGGAAAGCCCTCCTTTTTCAGAAATGTGGTATGGCTTATCAAAAAGAACAGTGCATACCCAACAATAAAGAGGAGCTACAATAATACCAACCAAGAAGATCTTTTGGTACTGTGGGGGATTCACCATCCTAATGATGCGGCAGAGCAGACAAAGCTCTATCAAAACCCAATCACCTATATTTCCGTTGGAACATCAACACTAAACCAGAGATTGGTACCAAAAATAGCTACCAGATCCAAAGTAAACGGGCAAAGTGGAAGGATGGAGTTCTTCTGGACAATTTTAAAACCGAATGATTCAATCAACTTCGAGAGTAATGGAAATTTCATTGCTCCAGAATATGCATACAAAATTGTCAAGAAAGGGGACTCAGCAATTATGAAAAGCGAATTGGAATATGGTAACTGCAACACCAAGTGTCAAACTCCAATGGGGGCGATAAACTCTAGTATGCCATTCCACAACATACACCCTCTCACCATCGGGGAATGCCCCAAATATGTGAAATCAAACAGATTAGTCCTTGCGACTGGGCTCAGAAATAGCCCTCAAAGAGAGAGAAGAAGAAAGAAGAGAGGACTATTTGGAGCTATAGCAGGTTTTATAGAGGGAGGATGGCAGGGAATGGTAGATGGTTGGTATGGATACCACCATAGCAATGAGCAGGGGAGTGGATACGCTGCAGACAAAGAATCCACTCAAAAGGCAATAGATGGAGTCACCAATAAGGTCAACTCGATCATTGACAAAATGAACACTCAGTTTGAGGCCGTTGGAAGGGAATTTAATAACTTAGAAAGGAGAATAGAGAATTTAAACAAGAAGATGGAAGACGGATTCCTAGATGTCTGGACTTATAATGCTGAACTTCTGGTTCTCATGGAAAATGAGAGAACTCTAGACTTTCATGACTCAAATGTCAAGAACCTTTACGACAAGGTCCGACTACAGCTTAGGGATAATGCAAAAGAGCTAGGTAACGGTTGTTTCGAGTTCTATCACAAATGTGATAATGAATGCATGGAAAGTGTAAGAAACGGAACGTATGACTACCCGCAATATTCAGAAGAAGCAAGGCTAAAAAGAGAGGAAATTAGTGGAGTAAAATTGGAATCAATAGGAACTTACCAAATACTGTCAATTTATTCAACAGTGGCAAGTTCCCTAGCGCTGGCAATCATGGTAGCTGGTCTATCTTTATGGATGTGCTCCAATGGTTCGTTACAATGCAGAATT
+ 'PEREGRINEFALCON_HK_D0028_2004' ATGGAGAAAATAGTGCTTCTTCTTGCAATAGTCAGTCTTGTTAAAAGTGATCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACACAATAATGGAAAAGAATGTTACTGTTACACATGCCCAAGACATACTGGAAAAGACACACAATGGGAAGCTCTGTGACCTAGATGGGGTGAAGCCTCTAATTTTGAGAGATTGTAGTGTCGCTGGATGGCTCCTCGGGAACCCAATGTGTGACGAATTCATCAATGTACCGGAATGGTCTTACATAGTGGAGAAGGCCAGTCCAGCCAATGACCTCTGTTACCCAGGTGATTTCAACGATTATGAAGAACTGAAACACCTATTGAGCAGAATAAACCATTTTGAGAAAATTCAGATCATCCCCAAAAGTTCTTGGTCCAATCATGAAGCCTCATCAGGGGTGAGCTCAGCATGTCCATACCTGGGAAAGCCCTCCTTTTTCAGAAATGTGGTATGGCTTATCAAAAAGAACAGTGCATACCCAACAATAAAGAGGAGCTACAATAATACCAACCAAGAAGATCTTTTGGTACTGTGGGGGATTCACCATCCTAATGATGCGGCAGAGCAGACAAAGCTCTATCAAAACCCAACCACCTATGTTTCCGTTGGAACATCAACACTAAACCAGAGATTGGTACCAAAAATAGCCACCAGATCCAAAGTAAACGGGCAAAGTGGAAGGATGGAGTTCTTCTGGACAATTTTAAAACCGAATGATGCAATCAACTTCGAGAGTAATGGAAATTTCATTGCTCCAGAATATGCATACAAAATTGTCAAGAAAGGGGACTCAGCAATTATGAAAAGTGAATTGGAATATGGTAACTGCAATACCAAGTGTCAAACTCCAATGGGGGCGATAAACTCTAGTATGCCATTCCACAACATACACCCTCTCACCATCGGGGAATGCCCCAAATATGTGAAATCAAACAGATTAGTCCTTGCGACTGGGCTCAGAAATAGCCCTCAAAGAGAGAGAAGAAGAAAAAAGAGAGGACTATTTGGAGCTATAGCAGGTTTTATAGAGGGAGGATGGCAGGGAATGGTAGATGGTTGGTATGGATACCACCATAGCAATGAGCAGGGGAGTGGATACGCTGCAGACAAAGAATCCACTCAAAAGGCAATAGATGGAGTCACCAATAAGGTCAACTCGATCATTGACAAAATGAACACTCAGTTTGAGGCCGTTGGAAGGGAATTTAATAACTTAGAAAGGAGAATAGAGAATTTAAACAAGAAGATGGAAGACGGATTCCTAGATGTCTGGACTTATAATGCTGAACTTCTGGTTCTCATGGAAAATGAGAGAACTCTAGACTTTCATGACTCAAATGTCAAGAACCTTTACGACAAGGTCCGACTACAGCTTAGGGATAATGCAAAAGAGCTGGGTAACGGTTGTTTCGAGTTCTATCACAAATGTGATAATGAATGTATGGAAAGTGTAAGAAACGGAACGTATGACTACCCGCAGTATTCAGAAGAAGCAAGACTAAAAAGAGAGGAAATAAGTGGAGTAAAATTGGAATCAATAGGAACTTACCAAATACTGTCAATTTATTCAACAGTGGCGAGTTCCCTAGCGCTGGCAATCATGGTAGCTGGTCTATCTTTATGGATGTGCTCC------------------------
+ 'CK_HK_WF157_2003' ATGGAGAAAATAGTGCTTCTTCTTGCAATAGTCAGTCTTGTTAAAAGTGATCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACACAATAATGGAAAAGAACGTTACTGTTACACATGCCCAAGACATACTGGAAAAGACCCACAACGGGAAGCTCTGCGACCTAGATGGAGTGAAGCCTCTAATTTTGAGAGATTGTAGTGTAGCTGGATGGCTCCTCGGGAACCCAATGTGTGACGAATTCATCAATGTACCGGAATGGTCTTACATAGTGGAGAAGGCCAGTCCATCCAATGACCTCTGTTACCCAGGGGATTTCAACAATTATGAAGAACTGAAACACCTATTGAGCAGAATAAACCATTTTGAGAAAATTCAGATCATCCCCAAAAGCTCTTGGTCCAATCATGAAGCCTCATCAGGGGTGAGCTCAGCATGTCCATACCTGGGAAAGCCCTCCTTTTTCAGAAATGTGGTATGGCTTATCAAAAAGAACAGTACATACCCAACAATAAAGAGGAGCTACAATAATACCAACCAAGAAGATCTTTTGGTACTGTGGGGGATTCACCATCCTAATGATGCGGCAGAGCAGATAAAGCTCTATCAAAACCCAACCACCTATATTTCCGTTGGAACATCAACACTAAACCAGAGATTGGTACCAAAAATAGCTACTAGATCCAAAGTAAACGGGCAAAGTGGAAGGATGGAGTTCTTCTGGACAATTTTAAAACCGAATGATGCAATCAACTTCGAGAGTAATGGAAATTTCATTGCTCCAGAATATGCATACAAAATTGTCAAGAAAGGGGACTCAGCAATTATGAAAAGTGAATTGGAATATGGTAACTGCAACACCAAGTGTCAAACTCCAATGGGGGCGATAAACTCTAGTATGCCCTTCCACAACATACACCCTCTCACCATCGGGGAATGCCCCAAATATGTGAAATCAAACAGACTAGTCCTTGCGACTGGGCTCAGAAATAGCCCTCAAAGAGAGAGAAGAAGAAAAAAGAGAGGACTATTTGGAGCTATAGCGGGTTTTATAGAGGGAGGATGGCAGGGAATGGTAGATGGTTGGTATGGATACCACCATAGCAATGAGCAGGGGAGTGGATACGCTGCAGACAAAGAATCCACTCAAAAGGCAATAGATGGAGTCACCAATAAGGTCAACTCGATCATTGACAAAATGAACACTCAGTTTGAGGCCGTTGGAAGGGAATTTAATAACTTAGAAAGGAGAATAGAGAATTTAAACAAGAAGATGGAAGACGGATTCCTAGATGTCTGGACTTATAATGCTGAACTTCTAGTTCTCATGGAAAATGAGAGAACTCTAGACTTTCATGACTCAAATGTCAAGAACCTTTACGACAAGGTCCGACTACAGCTTAGGGATAATGCAAAAGAGCTGGGTAACGGTTGTTTCGAGTTCTATCACAAATGTGATAATGAATGTATGGAAAGTGTAAGAAACGGAACGTATGACTACTCGCAGTATTCAGAAGAAGCAAGACTAAAAAGAGAGGAAATAAGTGGAGTAAAATTGGAATCAATAGGAACTTACCAAATACTGTCAATTTATTCAACAGTGGCGAGTTCCCTAGCACTGGCAATCATGGTAGCTGGTCTATCTTTATGGATGTGCTCCAATGGTTCGTTACAATGT------
+ 'HUMAN_VIETNAM_CL105_2005' ATGGAGAAAATAGTGCTTCTTTTTGCGATAGTCAGTCTTGTTAAAAGTGATCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACACAATAATGGAAAAGAACGTTACTGTTACACATGCCCAAGACATACTGGAAAAGACACACAACGGGAAGCTCTGCGATCTAGATGGAGTGAAGCCTCTAATTTTGAGAGATTGTAGTGTAGCTGGATGGCTACTCGGAAACCCAATGTGTGACGAATTCATCAATGTGCCGGAATGGTCTTACATAGTGGAGAAGGTCAATCCAGTCAATGACCTCTGTTACCCAGGGGTTTTCAATGACTATGAAGAATTGAAACACCTATTGAGCAGAATAAACCATTTTGAGAAAATTCAGATCATCCCCAAAAGTTCTTGGTCCAGTCATGAAGCCTCATTAGGGGTGAGCTCAGTATGTCCATACCAGGGAAAGTCCTCCTTTTTCAGAAATGTGGTATGGCTTATCAAAAAGAACAGTACATACCCAACAATAAAGAGGAGCTACAATAATACCAACCAAGAAGATCTTTTGGTAATATGGGGGATTCATCATCCTAATGATGCGGCAGAGCAGATAAAGCTCTATCAAAACCCAACCACCTATATTTCCGTTGGGACATCAACACTAAACCAGAGATTGGTACCAAGAATAGCTACTAGATCCAAAGTAAACGGGCAAAGTGGGAGGATGGAGTTCTTCTGGACAATTTTAAAACCGAATGATGCAATCAACTTCGAGAGTAATGGAAATTTCATTGCTCCAGAATATGCATACAAGATTGTCAAGAAAGGGGACTCAACAATTATGAAAAGTGAATTGGAATATGGTAACTGCAACACCAAGTGTCAAACTCCAATGGGGGCGATAAACTCTAGTATGCCATTCCACAATATACACCCTCTCACCATCGGGGAATGCCCCAAATATGTGAAATCAAACAGATTAGTCCTTGCGACTGGGCTCAGAAATAGCCCTCAAAAAGAGAGAAGAAGAAAAAAGAGAGGATTATTTGGAGCTATAGCAGGTTTTATAGAGGGAGGATGGCAGGGAATGGTAGATGGTTGGTATGGGTACCACCATAGCAATGAGCAGGGGAGTGGGTACGCTGCAGACAAAGAATCCACTCAAAAGGCAATAGATGGAGTCACCAATAAGGTCAACTCGATCATTGACAAAATGAACACTCAGTTTGAGGCCGTTGGAAGGGAATTTAACAACTTAGAAAGGAGAATAGAGAATTTAAACAAGAAGATGGAAGACGGGTTCCTAGATGTCTGGACTTATAATGCTGAACTTCTGGTTCTCATGGAAAATGAGAGAACTCTAGACTTTCATGACTCAAATGTCAAGAACCTTTACGACAAGGTCCGACTACAGCTTAGGGATAATGCAAAGGAGCTGGGTAACGGTTGTTTCGAGTTCTATCATAAATGTGATAATGAATGTATGGAAAGTGTAAGAAACGGAACGTATGACTACCCGCAGTATTCAGAAGAAGCAAGATTAAAAAGAGAGGAAATAAGTGGAGTAAAATTGGAATCAATAGGAATTTACCAAATACTGTCAATTTATTCTACAGTGGCGAGTTCCCTAGCACTGGCAATCATGATAGCTGGTCTATCCTTATGGATGTGCTCCAATGGGTCGTTACAA---------
'DUCK_VIETNAM_376_2005' ATGGAGAAAATAGTGCTTCTTTTTGCGATAGTCAGTCTTGTTAAAAGTGATCAGATTTGCATTGGTTACCATGCAAACAACTCAACAGAGCAGGTTGACACAATAATGGAAAAGAACGTTACTGTTACACATGCCCAAGACATACTGGAAAAGACACACAACGGGAAGCTCTGCGATCTAGATGGAGTGAAGCCTCTAATTTTGAGAGATTGTAGTGTAGCTGGATGGCTCCTCGGAAACCCAATGTGTGACGAATTCATCAATGTGCCGGAATGGTCTTACATAGTGGAGAAGGCCAATCCAGTCAATGACCTCTGTTACCCAGGGGATTTCAATGACTATGAAGAATTGAAACACCTATTGAGCAGAATAAACCATTTTGAGAAAATTCAGATCATCCCCAAAAGTTCTTGGTCCAGTCATGAAGCCTCATTAGGAGTGAGCTCAGCATGTCCATACCAGGGAAATCCCTCCTTTTTCAGAAATGTGGTATGGCTTATCAAAAAGAACAGTACATACCCAACAATAAAGAGGAACTACAATAATACCAACCAAGAAGATCTTTTGGTAATGTGGGGGATTCACCATCCTAATGATGCGGCAGAGCAGACAAAGCTCTATCAAAACCCAACCACCTATATTTCCGTTGGGACATCAACACTAAACCAGAGATTGGTACCAAGAATAGCTACTAGATCCAAAATAAACGGGCAAAGTGGGAGGATAGAGTTCTTCTGGACAATTTTAAAACCGAATGATGCAATCAACTTCGAGAGTAATGGAAATTTCATTGCTCCAGAATATGCATACAAAATTGTCAAGAAAGGGGACTCAACAATTATGAAAAGTGAATTGGAATATGGTAACTGCAACACCAAGTGTCAAACTCCAATGGGGGCGATAAACTCTAGTATGCCATTCCACAATATACATCCTCTCACCATCGGGGAGTGCCCCAAATATGTGAAATCAAACAGATTAGTCCTTGCGACTGGGCTCAGAAATAGCCCTCAAAGAGAGAGAAGAAGAAAAAAGAGAGGATTATTTGGAGCTATAGCAGGTTTTATAGAAGGAGGATGGCAAGGAATGGTAGATGGTTGGTATGGGTACCACCATAGCAATGAGCAGGGAAGTGGGTACGCTGCAGACAAAGAATCCACTCAAAAGGCAATAGATGGAGTCACCAATAAGGTCAACTCGATCATTGACAAAATGAACACTCAGTTTGAGGCCGTTGGAAGGGAATTTAACAACTTAGAAAGGAGAATAGAGAATTTAAACAAGAAGATGGAAGACGGGTTCCTAGATGTCTGGACTTATAATGCTGAACTTCTGGTTCTCATGGAAAATGAGAGAACTCTAGACTTTCATGACTCAAATGTCAAGAACCTTTACGACAAGGTCCGACTACAGCTTAGAGATAATGCAAAGGAGCTGGGTAACGGTTGTTTCGAGTTCTATCATAAATGTGATAATGAATGTATGGAAAGTGTAAGAAACGGAACGTATGACTACCCGCAGTATTCAGAAGAAGCAAGATTAAAAAGAGAGGAAATAAGTGGAGTAAAATTGGAATCAATAGGAATTTACCAAATACTGTCAATTTATTCTACTGTGGCGAGTTCCCTAGCACTGGCAATCATGGTAGCTGGTCTATCCTTATGGATGTGCTCCAATGGGTCGTTACAATGCAGA---
+ 'VIETNAM_3062_2004' ATGGAGAAAATAGTGCTTCTTTTTGCAATAGTCAGTCTTGTTAAAAGTGATCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACACAATAATGGAAAAGAACGTTACTGTTACACATGCCCAAGACATACTGGAAAAGACACACAACGGGAAGCTCTGCGATCTAGATGGAGTGAAGCCTCTAATTTTGAGAGATTGTAGTGTAGCTGGATGGCTCCTCGGAAACCCAATGTGTGACGAATTCATCAATGTGCCGGAATGGTCTTACATAGTGGAGAAGGCCAATCCAGTCAATGACCTCTGTTACCCAGGGGATTTCAATGACTATGAAGAATTGAAACACCTATTGAGCAGAATAAACCATTTTGAGAAAATTCAGATCATCCCCAAAAGTTCTTGGTCCAGTCATGAAGCCTCATTAGGAGTGAGCTCAGCATGTCCATACCAGGGAAAGTCCTCCTTTTTCAGAAATGTGGTATGGCTTATCAAAAAGAACAGTACATACCCAACAATAAAGAGGAGCTACAATAATACCAACCAAGAAGATCTTTTGGTACTGTGGGGGATTCACCATCCTAATGATGCGGCAGAGCAGACAAAGCTCTATCAAAACCCAACCACCTATATTTCCGTTGGGACATCAACACTAAACCAGAGGTTGGTACCAAGAATAGCTACTAGATCCAAAGTAAACGGGCAAAGTGGAAGGATGGAGTTCTTCTGGACAATTTTAAAACCGAATGATGCAATCAACTTCGAGAGTAATGGAAATTTCATTGCTCCAGAATATGCATACAAAATTGTCAAGAAAGGGGACTCAACAATTATGAAAAGTGAATTGGAATATGGTAACTGCAACACCAAGTGTCAAACTCCAATGGGGGCGATAAACTCTAGTATGCCATTCCACAATATACACCCTCTCACCATCGGGGAATGCCCCAAATATGTGAAATCAAACAGATTAGTCCTTGCGACTGGGCTCAGAAATAGCCCTCAAAGAGAGAGAAGAAGAAAAAAGAGAGGATTATTTGGAGCTATAGCAGGTTTTATAGAGGGAGGATGGCAGGGAATGGTAGATGGTTGGTATGGGTACCACCATAGCAATGAGCAGGGGAGTGGGTACGCTGCAGACAAAGAATCCACTCAAAAGGCAATAGATGGAGTCACCAATAAGGTCAACTCGATCATTGACAAAATGAACACTCAATTTGAGGCCGTTGGAAGGGAATTTAACAACTTAGAAAGGAGAATAGAGAATTTAAACAAGAAGATGGAAGACGGGTTCCTAGATGTCTGGACTTATAATGCTGAACTTCTGGTTCTCATGGAAAATGAGAGAACTCTAGACTTTCATGACTCAAATGTCAAGAACCTTTACGACAAGGTCCGACTACAGCTTAGGGATAATGCAAAGGAGCTGGGTAACGGTTGTTTCGAGTTCTATCATAAATGTGATAATGAATGTATGGAAAGTGTAAGAAACGGAACGTATGACTACCCGCAGTATTCAGAAGAAGCAAGACTAAAAAGAGAGGAAATAAGTGGAGTAAAATTGGAATCAATAGGAATTTACCAAATACTGTCAATTTATTCTACAGTGGCGAGTTCCCTAGCACTGGCAATCATGGTAGCTGGTCTATCCTTATGGATGTGCTCCAATGGGTCG---------------
'MALLARD_VIETNAM_16_2003' ATGGAGAAAATAGTGCTTCTTTTTGCAATAGTCAGTCTTGTTAAAAGTGATCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACACAATAATGGAAAAGAACGTTACTGTTACACATGCCCAAGACATACTGGAAAAGACACACAACGGGAAGCTCTGCGATCTAGATGGAGTGAAGCCTCTAATTTTGAGAGATTGTAGTGTAGCTGGATGGCTCCTCGGAAACCCAATGTGTGACGAATTCATCAATGTGCCGGAATGGTCTTACATAGTGGAGAAGGCCAATCCAGTCAATGACCTCTGTTACCCAGGGGATTTCAATGAATATGAAGAATTGAAACACCTATTGAGCAGAATAAACCATTTTGAGAAAATTCAGATCATCCCCAAAAGTTCTTGGTCCAGTCATGAAGCCTCATTAGGGGTGAGCTCAGCATGTCCATACCAGGGAAAGTCCTCCTTTTTCAGAAATGTGGTATGGCTTGTCAAAAAGAACAGTACATACCCAACAATAAAGAGGAGCTACAATAATACCAACCAAGAAGATCTTTTGGTACTGTGGGGGATTCACCATCCTAATGATGCGGCAGAGCAGACAAAGCTCTATCAAAATCCAACCACCTACATTTCCGTTGGGACATCAACACTAAACCAGAGATTGGTACCAAGAATAGCTACTAGATCCAAAGTAAACGGGCAAAGTGGAAGGATGGAGTTCTTCTGGACAATTTTAAAACCGAATGATGCAATCAACTTCGAGAGTAATGGAAATTTCATTGCTCCAGAATATGCATACAAAATTGTCAAGAAAGGGGACTCAACAATTATGAAAAGTGAATTGGAATATGGTAACTGCAACACCAAGTGTCAAACTCCAATGGGGGCGATAAACTCTAGTATGCCATTCCACAATATACACCCCCTCACCATCGGGGAATGCCCCAAATATGTGAAATCAAACAGATTAGTCCTTGCGACTGGGCTCAGAAATAGCCCTCAAAGAGAGAGAAGAAGAAAAAAGAGAGGATTATTTGGAGCTATAGCAGGTTTTATAGAGGGAGGATGGCAAGGAATGGTAGATGGTTGGTATGGGTACCACCATAGCAATGAGCAGGGGAGTGGGTACGCTGCAGACAAAGAATCCACTCAAAAGGCAATAGATGGAGTCACCAATAAGGTCAACTCGATCATTGACAAAATGAACACTCAGTTTGAGGCCGTTGGAAGGGAATTTAACAACTTAGAAAGGAGAATAGAGAATTTAAACAAGAAGATGGAAGACGGGTTCCTAGATGTCTGGACTTATAATGCTGAACTTCTGGTTCTCATGGAAAATGAGAGAACTCTAGACTTTCATGACTCAAATGTCAAGAACCTTTACGACAAGGTCCGACTACAGCTTAGGGATAATGCAAAGGAGCTGGGTAACGGTTGTTTCGAGTTCTATCATAAATGTGATAATGAATGTATGGAAAGTGTAAGAAACGGAACGTATGACTACCCGCAGTATTCAGAAGAAGCAAGACTAAAAAGAGAGGAAATAAGTGGAGTAAAATTGGAATCAATAGGAATTTACCAAATACTGTCAATTTATTCTACAGTGGCGAGTTCCCTAGCACTGGCAATCATGGTAGCTGGTCTATCCTTATGGATGTGCTCCAATGGGTCGTTACAATGCAGA---
'CHICKEN_THAILAND_KANCHANABURI_CK_160_2005' ATGGAGAAAATAGTGCTTCTTTTTGCAATAGTCAGTCTTGTTAAAAGTGATCAGATTTGCATTGGTTACCATGCAAACAACTCAACAGAGCAGGTTGACACAATAATGGAAAAGAACGTTACTGTTACACATGCCCAAGACATACTGGAAAAGACACACAACGGGAAGCTCTGTGATCTAGATGGAGTGAAGCCTCTAATTTTGAGAGATTGTAGTGTAGCTGGATGGCTCCTTGGAAACCCAATGTGTGATGAATTCATCAATGTGCCGGAATGGTCTTACATAGTGGAGAAGGCCAATCCAGCCAATGACCTCTGTTACCCAGGGGATTTCAATGACTATGAAGAATTGAAACACCTATTGAGCAGAATAAACCATTTTGAGAAAATTCAGATCATCCCCAAAAGTTCTTGGTCCAGTCATGAAGCCTCATTAGGAGTGAGCTCAGCATGTCCATATCAGGGAAAGTCCTCCTTTTTCAGAAATGTGGTATGGCTTATCAAAAAGAACAGTACATACCCAACAATAAAGAGGAGCTACAATAATACCAACCAAGAAGATCTTTTGGTACTGTGGGGGATTCACCATCCTAATGATGCGGCAGAGCAGACAAAGCTCTATCAAAACCCAACCACCTACATTTCCGTTGGGACATCAACACTAAACCAGAGATTGGTACCAAGAATAGCTACTAGATCCAAAGTAAACGGGCAAAGTGGAAGGATGGAGTTCTTCTGGACAATTTTAAAACCGAATGATGCAATCAACTTCGAGAGTAATGGAAATTTCATTGCTCCAGAATATGCATACAAAATTGTCAAGAAAGGGGACTCAACAATTATGAAAAGTGAATTGGAATATGGTAACTGCAACACCAAGTGTCAAACTCCAATGGGGGCGATAAACTCTAGTATGCCATTCCACAATATACACCCTCTCACCATCGGGGAATGCCCCAAATATGTGAAATCAAACAGATTAGTCCTTGCGACTGGACTCAGAAATAGCCCTCAAAGAGAGAAAAGAAGAAAAAAGAGAGGATTATTTGGAGCTATAGCAGGTTTTATAGAGGGAGGATGGCAGGGAATGGTAGATGGTTGGTATGGGTACCACCATAGCAATGAGCAGGGGAGTGGGTACGCTGCAGACAAAGAATCCACTCAAAAGGCAATAGATGGAGTCACCAATAAGGTCAACTCGATCATTGACAAAATGAACACTCAGTTTGAGGCCGTTGGAAGGGAATTTAACAACTTAGAAAGGAGAATAGAGAATTTAAACAAGAAGATGGAAGACGGGTTCCTAGATGTCTGGACTTATAATGCTGAACTTCTGGTTCTCATGGAAAATGAGAGAACTCTAGACTTTCATGACTCAAATGTCAAGAACCTTTACGACAAGGTCCGACTACAGCTTAGGGATAATGCAAAGGAGCTGGGTAACGGTTGTTTCGAGTTCTATCATAAATGTGATAATGAATGTATGGAAAGTGTAAGGAACGGAACGTATGACTACCCGCAGTATTCAGAAGAAGCAAGACTAAAAAGAGAGGAAATAAGTGGAGTAAAATTGGAATCAATAGGAATTTACCAAATACTGTCAATTTATTCTACAGTAGCGAGTTCCCTAGCACTGGCAATCATGGTAGCTGGTCTATCCTTATGGATGTGCTTCAATGGGTCGTTACAATGCAGAATT
- 'DUCK_GUANGZHOU_20_2005' ATGGAGAAAATAGTGCTTCTTCTTGCAATAGTCAGTCTTGTTAAAAGTGATCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACACAATAATGGAAAAGAACGTTACTGTTACACATGCCCAAGACATACTGGAAAAGACACACAATGGGAAGCTCTGCGACCTAGATGGGGTGAAGCCTCTAATTTTGAGAGATTGTAGTGTAGCTGGATGGCTCCTCGGGAACCCAATGTGTGACGAATTCATCAATGTACCGGAATGGTCTTACATAGTGGAGAAGGCCAATCCAGCCAATGACCTCTGTTACCCAGGTGATTTCAACGATTATGAAGAACTGAAACACCTATTGAGCAGAATAAACCATTTTGAGAAAATTCAGATCATCCCCAAAAGTTCTTGGTCCAACCATGAATCCTCATCAGGGGTGAGCTCAGCATGTCCATACCTGGGAAAGCCCTCCTTTTTCAGAAATGTGGTATGGCTTATCAAAAAGAACAATGCATACCCAACAATAAAGAAGAGCTACAATAATACCAACCAAGAAGATCTTTTGGTACTGTGGGGGATTCACCATCCTAATGATGCGACAGAGCAGACAAAGCTCTATCAAAACCCAACCACTTATATTTCCGTTGGAACATCAACACTAAACCAGAGATTGGTACCAAAAATAGCTACCAGATCCAAAGTAAACGGGCAAAGTGGAAGGATGGAGTTCTTCTGGACAATTTTAAAACCGAATGATGCAATCAACTTCGAGAGTAATGGAAATTTCATTGCTCCAGAATATGCATACAAAATTGTCAAGAAAGGGGACTCAGCAATTATGAAAAGTGAATTGGAATATGGTAACTGCAACACCAAATGTCAAACTCCAATGGGGGCGATAAACTCTAGTATGCCATTCCACAACATACACCCTCTCACCATCGGGGAATGCCCCAAATATGTGAAATCAAACAGATTAGTCCTTGCGACTGGGCTCAGAAATAGCCCTCAAAGGGAGAGAAGAAGAAAGAAGAGAGGACTATTTGGAGCTATAGCAGGTTTTATAGAGGGAGGATGGCAGGGAATGGTAGATGGTTGGTATGGATACCACCATAGCAATGAGCAGGGGAGTGGATACGCTGCAGACAAAGAATCCACTCAAAAGGCAATAGATGGAGTCACCAATAAGGTCAACTCGATCATTGACAAAATGAACACTCAGTTTGAGGCCGTTGGAAGGGAATTTAATAACTTAGAAAGGAGAATAGAGAATTTAAACAAGAAGATGGAAGACGGATTCCTAGATGTCTGGACTTATAATGCTGAACTTCTGGTTCTCATGGAAAATGAGAGAACTCTAGACTTTCATGACTCAAATGTCAGGAACCTTTACGACAAGGTCCGACTACAGCTTAGGGATAATGCAAAAGAGCTGGGTAACGGTTGTTTCGAGTTCTATCACAAATGTGATGATGAATGCATGGAAAGTGTAAGAAACGGAACGTATGACTACCCGCAGTATTCAGAAGAAGCAAGGCTAAAAAGAGAGGAAATAAGTGGAGTAAAATTGGAATCAATAGGAACTTACCAAATACTGTCAATTTATTCAACAGTGGCAAGTTCCCTAGCGCTGGCAATCATGGTAGCTGGTCTATCTTTATGGATGTGCTCCAATGGTTCGTTACAATGCAGAATT
- 'CK_HK_WF157_2003' ATGGAGAAAATAGTGCTTCTTCTTGCAATAGTCAGTCTTGTTAAAAGTGATCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACACAATAATGGAAAAGAACGTTACTGTTACACATGCCCAAGACATACTGGAAAAGACCCACAACGGGAAGCTCTGCGACCTAGATGGAGTGAAGCCTCTAATTTTGAGAGATTGTAGTGTAGCTGGATGGCTCCTCGGGAACCCAATGTGTGACGAATTCATCAATGTACCGGAATGGTCTTACATAGTGGAGAAGGCCAGTCCATCCAATGACCTCTGTTACCCAGGGGATTTCAACAATTATGAAGAACTGAAACACCTATTGAGCAGAATAAACCATTTTGAGAAAATTCAGATCATCCCCAAAAGCTCTTGGTCCAATCATGAAGCCTCATCAGGGGTGAGCTCAGCATGTCCATACCTGGGAAAGCCCTCCTTTTTCAGAAATGTGGTATGGCTTATCAAAAAGAACAGTACATACCCAACAATAAAGAGGAGCTACAATAATACCAACCAAGAAGATCTTTTGGTACTGTGGGGGATTCACCATCCTAATGATGCGGCAGAGCAGATAAAGCTCTATCAAAACCCAACCACCTATATTTCCGTTGGAACATCAACACTAAACCAGAGATTGGTACCAAAAATAGCTACTAGATCCAAAGTAAACGGGCAAAGTGGAAGGATGGAGTTCTTCTGGACAATTTTAAAACCGAATGATGCAATCAACTTCGAGAGTAATGGAAATTTCATTGCTCCAGAATATGCATACAAAATTGTCAAGAAAGGGGACTCAGCAATTATGAAAAGTGAATTGGAATATGGTAACTGCAACACCAAGTGTCAAACTCCAATGGGGGCGATAAACTCTAGTATGCCCTTCCACAACATACACCCTCTCACCATCGGGGAATGCCCCAAATATGTGAAATCAAACAGACTAGTCCTTGCGACTGGGCTCAGAAATAGCCCTCAAAGAGAGAGAAGAAGAAAAAAGAGAGGACTATTTGGAGCTATAGCGGGTTTTATAGAGGGAGGATGGCAGGGAATGGTAGATGGTTGGTATGGATACCACCATAGCAATGAGCAGGGGAGTGGATACGCTGCAGACAAAGAATCCACTCAAAAGGCAATAGATGGAGTCACCAATAAGGTCAACTCGATCATTGACAAAATGAACACTCAGTTTGAGGCCGTTGGAAGGGAATTTAATAACTTAGAAAGGAGAATAGAGAATTTAAACAAGAAGATGGAAGACGGATTCCTAGATGTCTGGACTTATAATGCTGAACTTCTAGTTCTCATGGAAAATGAGAGAACTCTAGACTTTCATGACTCAAATGTCAAGAACCTTTACGACAAGGTCCGACTACAGCTTAGGGATAATGCAAAAGAGCTGGGTAACGGTTGTTTCGAGTTCTATCACAAATGTGATAATGAATGTATGGAAAGTGTAAGAAACGGAACGTATGACTACTCGCAGTATTCAGAAGAAGCAAGACTAAAAAGAGAGGAAATAAGTGGAGTAAAATTGGAATCAATAGGAACTTACCAAATACTGTCAATTTATTCAACAGTGGCGAGTTCCCTAGCACTGGCAATCATGGTAGCTGGTCTATCTTTATGGATGTGCTCCAATGGTTCGTTACAATGT------
- 'SWINE_ANHUI_2004' ATGGAGAAAATAGTGCTTCTTCTTGCAATAGTCAGTCTTGTTAAAGGTGATCAGATTTGCACTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACACAATAATGGAAAAGAACGTTACTGTTACACATGCTCAAGACATACTGGAAAAGACACACAACGGGAAGCTCTGCGACCTAGATGGAGTGAAGCCTCTAATTTTAAGAGATTGTAGTGTAGCTGGATGGCTCCTCGGGAACCCAATGTGTGACGAATTCATCAATGTGCCGGAATGGTCTTACATAGTGGAGAAGGCCAATCCAGCCAATGACCTCTGTTACCCAGGGGATTTCAACGACTATGAAGAACTGAAACACCTATTGAGCAGAATAAACCATTTTGAGAAAATTCAGATCATCCCCAAAAGTTCTTGGTCCGATCATGAAGCCTCATCAGGGGTGAGCTCAGCATGTCCATACCAGGGAAGGTCCTCCTTTTTCAGAAATGTGGTATGGCTTATCAAAAAGAACAGTGCATACCCAACAATAAAGAGGAGCTACAATAATACCAACCAAGAAGATCTTTTGGTACTGTGGGGGATTCACCACCCTAATGATGCGGCAGAGCAGATAAAGCTCTATCAAAACCCAACCACCTATATTTCCGTTGGGACATCAACACTAAACCAGAGATTGGTACCAAAAATAGCTACTAGATCCAAAGTAAACGGACAAAGTGGAAGAATGGAGTTCTTCTGGACAATTTTAAAACCGAATGATGCTATCAATTTCGAGAGTAATGGAAATTTCATTGCTCCAGAATATGCATACAAAATTGTCAAGAAAGGGGACTCTGCAATTATGAAAAGTGAATTGGAATATGGCAACTGCAACACCAAGTGTCAAACTCCAGTGGGGGCGATAAATTCTAGCATGCCATTCCACAACATACACCCTCTCACCATCGGGGAATGCCCCAAATATGTGAAATCAAACAGATTAGTCCTTGCGACTGGACTCAGAAATGCCCCTCAAAGAGAGGGAAGAAGAAAAAAGAGAGGACTATTTGGAGCTATAGCAGGGTTTATAGAGGGAGGATGGCAGGGGATGGTAGATGGTTGGTATGGGTACCACCATAGCAATGAGCAGGGGAGTGGATACGCTGCAGACAAAGAATCCACTCAAAAAGCAATAGATGGAGTCACCAATAAGGTCAACTCGATCATTGACAAAATGAACACTCAGTTTGAGGCCGTTGGAAGGGAATTTAATAACTTAGAAAGGAGAATAGAAAATTTAAACAAGAAGATGGAGGACGGATTCCTAGATGTCTGGACTTATAATGCTGAACTTCTGGTTCTCATGGAAAATGAGAGAACTCTAGACTTTCATGACTCAAATGTCAAGAACCTTTACGACAAGGTCCGACTACAGCTTAGGGATAATGCAAAGGAGCTGGGTAACGGTTGTTTCGAGTTCTATCACAGATGTGATAATGAATGTATGGAAAGTGTAAGAAACGGAACGTATGACTACCCGCAGTATTCGGAAGAAGCAAGACTAAACAGAGAGGAAATAAGTGGAGTAAAATTGGAATCAATAGGAACTTACCAAATACTGTCAATTTATTCAACAGTGGCGAGTTCCCTAGCACTGGCAATCATGGTGGCTGGTCTATCTTTATGGATGTGCTCCAATGGATCGTTACAATGCAGAATT
- 'DUCK_VIETNAM_272_2005' ATGGAGAAAATAGTGCTTCTTTTTGCAATAGTCAGTCTTGTTAAAAGTGATCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACACAATAATGGAAAAGAACGTTACTGTTACACATGCCCAAGACATACTGGAAAAGACACACAACGGGAAGCTCTGCGATCTAGATGGAGTGAAGCCTCTAATTTTGAGAGATTGTAGTGTAGCTGGATGGCTCCTTGGAAATCCAATGTGTGACGAATTCATCAATGTGCCGGAATGGTCTTACATAGTGGAGAAGGCCAATCCAGTCAATGACCTCTGTTACCCAGGGGATTTCAATGACTATGAAGAATTGAAACACCTATTGAGCAGAATAAACCATTTTGAGAAAATTCAGATCATCCCCAAAAGTTCTTGGCCCAGTCATGAAGCCTCATTAGGGGTGAGCTCAGCATGTCCATACCAGGGAAGGTCCTCCTTTTTCAGAAATGTGGTATGGCTTATCAAAAAGAACAGTACATATCCAACAATAAAGAGGAGCTACAATAATACCAACCAAGAAGATCTTTTGGTACTGTGGGGGATTCACCATCCTAATGATGCGGCAGAGCAGACAAAGCTCTATCAAAACCCAACCACCTATATTTCCGTTGGGACATCAACACTAAACCAGAGATTGATACCAAGAATAGCTACTAGATCCAAAGTAAACGGGCAAAGTGGAAGGATGGAGTTCTTCTGGACAATTTTAAAACCGAATGATGCAATCAATTTCGAGAGTAATGGAAATTTCATTGCCCCAGAATACGCATACAAAATTGTCAAGAAAGGGGACTCAACAATTATGAAAAGTGAATTGGAATATGGTAACTGCAACACCAAGTGTCAAACACCAATGGGGGCGATAAATTCTAGTATGCCATTCCACAATATACACCCTCTCACCATCGGGGAATGCCCCAAATATGTGAAATCAAACAGATTAGTCCTTGCGACTGGGCTCAGAAATAGCCCTCAAAGAGAGAGAAGA---AAAAAGAGAGGATTATTTGGAGCTATAGCAGGTTTTATAGAGGGGGGATGGCAGGGAATGGTAGATGGTTGGTATGGGTACCACCATAGCAATGAACAGGGGAGTGGGTACGCTGCAGACAAAGAATCCACTCAAAAGGCAATAGATGGAGTCACCAATAAGGTCAACTCGATCATTGACAAAATGAACACTCAGTTTGAGGCCGTTGGAAGGGAATTTAACAACTTAGAAAGGAGAATAGAGAATTTAAACAAGAAGATGGAAGACGGGTTCCTAGATGTCTGGACTTATAATGCTGAACTTCTGGTTCTCATGGAAAATGAGAGAACTCTAGACTTTCATGACTCAAATGTCAAGAACCTTTACGACAAGGTCCGACTACAGCTTAGGGATAATGCAAAGGAGCTGGGTAACGGTTGTTTCGAGTTCTATCATAAATGTGATAATGAATGTATGGAAAGTGTAAGAAATGGAACGTATGACTACCCGCAGTATTCAGAAGAAGCAAAACTAAAAAGAGAGGAAATAAGTGGAGTAAAATTGGAATCAATAGGAATTTACCAAATACTGTCAATTTATTCCACAGTAGCGAGTTCCCTAGCACTGGCAATCATGGTAGCTGGTCTATCCTTATGGATGTGCTCCAATGGGTCGTTACAATGCAGA---
- 'HONGKONG_97_98' ------------------------------------------------GACCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGATACAATAATGGAAAAGAATGTTACTGTTACACATGCCCAAGACATACTGGAAAGGACACACGACGGGAAGCTCTGCGATCTAAATGGAGTGAAACCTCTCATTTTGAGGGATTGTAGTGTAGCTGGATGGCTCCTCGGAAACCCTATGTGTGACGAATTCATCAATGTGCCGGAATGGTCTTACATAGTGGAGAAGGCCAGTCCAGCCAATGACCTCTGTTATCCAGGGAATTTCAACGACTATGAAGAACTGAAACACCTATTGAGCAGAATAAACCATTTTGAGAAAATTCAGATCATCCCCAAAAGTTCTTGGTCCAATCATGATGCCTCATCAGGGGTGAGCTCAGCATGTCCATACCTTGGGAGGTCCTCCTTTTTCAGAAATGTGGTATGGCTTATCAAAAAGAACAGTGCATACCCAACAATAAAGAGGAGCTACAATAATACCAACCAAGAAGATCTTTTGGTACTGTGGGGGATTCACCATCCTAATGATGCGGCAGAGCAGACAAAGCTCTATCAAAATCCAACCACCTACATTTCCGTTGGAACATCAACACTGAATCAGAGATTGGTTCCAGAAATAGCTACTAGACCCAAAGTAAACGGGCAAAGTGGAAGAATGGAGTTCTTCTGGACAATTTTAAAGCCGAATGATGCCATCAATTTCGAGAGTAATGGAAATTTCATTGCCCCAGAATATGCATACAAAATTGTCAAGAAAGGGGACTCAACAATTATGAAAAGTGAATTGGAATATGGTAACTGCAACACCAAGTGTCAAACTCCAATGGGGGCGATAAACTCTAGTATGCCATTCCACAACATACACCCCCTCACCATCGGGGAATGCCCCAAATATGTGAAATCAAACAGATTAGTTCTTGCGACTGGACTCAGAAATACCCCTCATAGGGAGAGAAGAAGAAAAAAGAGAGGACTATTTGGAGCTATAGCAGGTTTTATAGAAGGAGGATGGCAGGGAATGGTAGATGGTTGGTATGGGTACCACCATAGCAATGAGCAGGGGAGTGGATACGCTGCAGACCAAGAATCCACTCAAAAGGCAATAGATGGAGTCACCAATAAGGTCAACTCGATCATTAACAAAATGAACACTCAGTTTGAGGCCGTTGGAAGGGAATTTAATAACTTAGAAAGGAGAATAGAGAATTTAAACAAGAAAATGGAAGACGGATTCCTAGATGTCTGGACTTACAATGCTGAACTTCTGGTTCTCATGGAAAATGAGAGAACTCTCGACTTTCATGACTCAAATGTCAAGAACCTTTACGACAAGGTCCGACTACAGCTTAGGGATAATGCAAAGGAACTGGGTAATGGTTGTTTCGAATTCTATCACAAATGTGATAATGAATGTATGGAAAGTGTAAAAAACGGAACGTATGACTACCCGCAGTATTCAGAAGAAGCAAGACTAAACAGAGAGGAAATAAGTGGAGTAAAATTGGAATCAATGGGAACTTACCAAATACTGTCAATTTATTCAACAGTGGCGAGTTCCCTAGCACTGGCAATCATGGTAGCTGGTCTATCTTTATGGATGTGCTCCAATGGATCGTTACAATGCAGAATT
- 'GOOSE_SHANTOU_2216_2005' ATGGAGAAAATAGTGCTTCTTCTTGCAATAATCAGCCTTGTTAAAAGTGATCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACACAATAATGGAAAAGAACGTTACTGTTACACATGCCCAAGACATACTGGAAAAGACACACAATGGGAAGCTCTGCGACTTAGATGGGGTGAAGCCTCTAATTTTGAGAGACTGTAGTGTAGCTGGATGGCTCCTCGGGAACCCAATGTGTGACGAATTCATCAATGTACCGGAATGGTCTTACATAGTGGAGAAGGCCAGTCCAGCCAATGACCTCTGTTACCCAGGTGATTTCAACGATTATGAAGAACTGAAACACCTATTGAGCAGAATAAACCATTTTGAGAAAATTCAGATCATCCCCAAAAGTTCTTGGTCCAATCATGAAGCCTCATCAGGGGTGAGCTCAGCATGTCCATACCTGGGAAAGCCCTCCTTTTTCAGAAATGTGGTATGGCTTATCAAAAAGAACAGTGCATACCCAACAATAAAGAGGAGCTACAATAATACCAACCAAGAAGATCTTTTGGTACTGTGGGGGATTCACCATCCTAATGATGCGGCAGAGCAGACAAAGCTCTATCAAAACCCAATCACCTATATTTCCGTTGGAACATCAACACTAAACCAGAGATTGGTACCAAAAATAGCTACCAGATCCAAAGTAAACGGGCAAAGTGGAAGGATGGAGTTCTTCTGGACAATTTTAAAACCGAATGATTCAATCAACTTCGAGAGTAATGGAAATTTCATTGCTCCAGAATATGCATACAAAATTGTCAAGAAAGGGGACTCAGCAATTATGAAAAGCGAATTGGAATATGGTAACTGCAACACCAAGTGTCAAACTCCAATGGGGGCGATAAACTCTAGTATGCCATTCCACAACATACACCCTCTCACCATCGGGGAATGCCCCAAATATGTGAAATCAAACAGATTAGTCCTTGCGACTGGGCTCAGAAATAGCCCTCAAAGAGAGAGAAGAAGAAAGAAGAGAGGACTATTTGGAGCTATAGCAGGTTTTATAGAGGGAGGATGGCAGGGAATGGTAGATGGTTGGTATGGATACCACCATAGCAATGAGCAGGGGAGTGGATACGCTGCAGACAAAGAATCCACTCAAAAGGCAATAGATGGAGTCACCAATAAGGTCAACTCGATCATTGACAAAATGAACACTCAGTTTGAGGCCGTTGGAAGGGAATTTAATAACTTAGAAAGGAGAATAGAGAATTTAAACAAGAAGATGGAAGACGGATTCCTAGATGTCTGGACTTATAATGCTGAACTTCTGGTTCTCATGGAAAATGAGAGAACTCTAGACTTTCATGACTCAAATGTCAAGAACCTTTACGACAAGGTCCGACTACAGCTTAGGGATAATGCAAAAGAGCTAGGTAACGGTTGTTTCGAGTTCTATCACAAATGTGATAATGAATGCATGGAAAGTGTAAGAAACGGAACGTATGACTACCCGCAATATTCAGAAGAAGCAAGGCTAAAAAGAGAGGAAATTAGTGGAGTAAAATTGGAATCAATAGGAACTTACCAAATACTGTCAATTTATTCAACAGTGGCAAGTTCCCTAGCGCTGGCAATCATGGTAGCTGGTCTATCTTTATGGATGTGCTCCAATGGTTCGTTACAATGCAGAATT
- 'TREESPARROW_HENAN_3_2004' ATGGAGAAAATAGTGCTTCTTCTTGCAATAGTCAGTCTTGTTAAAAGTGATCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACACTATAATGGAAAAGAACGTTACTGTTACACATGCCCAAGACATACTGGAAAAGACACACAACGGGAAGCTCTGCGATCTAGATGGAGTGAAGCCTCTAATTTTGAGAGATTGTAGTGTAGCTGGATGGCTCCTCGGAAACCCAATGTGTGACGAATTCATCAATGTGCCGGAATGGTCTTACATAGTGGAGAAGGCCAGTCCAGCCAATGACCTCTGTTACCCAGGGGATTTCAACGACTATGAAGAACTGAAACACCTATTGAGCAGAATAAACCATTTTGAGAAAATTCGGATCATCCCCAAAAGTTCTTGGTCCAATCATGATGCCTCATCAGGGGTGAGCTCAGCATGTCCATACCAGGGGAAGCCCTCCTTTTTCAGAAATGTGGTATGGCTTATCAAAAAGAACAGTACATACCCAACGATAAAGAGGAGCTACAATAATACCAACCCAGAAGATCTTTTGGTACTGTGGGGGATTCACCATCCTAATGATGCGGCAGAGCAGATAAAGCTCTATCAAAACCCAACCACCTATATTTCCGTTGGAACATCAACACTAAACCAGAGATTGGTACCAAAAATAGCTACTAGATCCAAAGTAAATGGGCAAAGTGGAAGAATGGAGTTCTTCTGGACAATTTTAAAGCCGAATGACGCTATCAACTTCGAGAGTAATGGAAATTTCATTGCTCCAGAATATGCATACAAAATTGTCAAGAAAGGGGACTCAGCAATTATGAAAAGTGAATTGGAATATGGTAACTGCAACACCAAGTGTCAAACTCCAATGGGGGCGATAAATTCTAGTATGCCATTCCACAACATACACCCTCTCACCATCGGGGAATGCCCCAAATATGTGAAATCAAACAGATTAGTCCTTGCGACAGGGCTCAGAAATAGCCCTCAAAGAGAGGGAAGAAGAAAAAAGAGAGGACTATTTGGAGCTATAGCAGGTTTTATAGAGGGAGGATGGCAGGGAATGGTAGATGGTTGGTATGGGTACCACCATAGCAATGAGCAGGGGAGTGGATACGCTGCAGACAAAGAATCCACTCAAAAAGCAATAGATGGAGTCACCAATAAGGTCAACTCGATCATTGACAAAATGAACACTCAGTTTGAGGCCGTTGGAAGGGAATTTAATAACTTAGAAAGGAGAATAGAAAATTTAAACAAGAAGATGGAGGACGGATTCCTAGATGTCTGGACTTATAATGCTGAACTTCTGGTTCTCATGGAAAATGAGAGAACTCTAGACTTTCATGACTCAAATGTCAAGAACCTTTACGAAAAGGTCCGACTACAACTTAGGGATAATGCAAAGGAGCTGGGTAACGGTTGTTTCGAGTTCTATCACAAATGTGATAATGAATGTATGGAAAGTGTAAAAAACGGAACGTATGACTACCCGCAGTATACGGAAGAAGCAAGACTAAACAGAGAGGAAATAAGTGGAGTAAAATTGGAATCAATAGGAACTTACCAAATACTGTCAATTTATTCAACAGTAGTGAGTTCCCTAGCACTGGCAATCATGGTAGCTGGTCTATCTTTATGGATGTGCTCCAATGGATCGTTACAATGCAGAATT
- 'PEREGRINEFALCON_HK_D0028_2004' ATGGAGAAAATAGTGCTTCTTCTTGCAATAGTCAGTCTTGTTAAAAGTGATCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACACAATAATGGAAAAGAATGTTACTGTTACACATGCCCAAGACATACTGGAAAAGACACACAATGGGAAGCTCTGTGACCTAGATGGGGTGAAGCCTCTAATTTTGAGAGATTGTAGTGTCGCTGGATGGCTCCTCGGGAACCCAATGTGTGACGAATTCATCAATGTACCGGAATGGTCTTACATAGTGGAGAAGGCCAGTCCAGCCAATGACCTCTGTTACCCAGGTGATTTCAACGATTATGAAGAACTGAAACACCTATTGAGCAGAATAAACCATTTTGAGAAAATTCAGATCATCCCCAAAAGTTCTTGGTCCAATCATGAAGCCTCATCAGGGGTGAGCTCAGCATGTCCATACCTGGGAAAGCCCTCCTTTTTCAGAAATGTGGTATGGCTTATCAAAAAGAACAGTGCATACCCAACAATAAAGAGGAGCTACAATAATACCAACCAAGAAGATCTTTTGGTACTGTGGGGGATTCACCATCCTAATGATGCGGCAGAGCAGACAAAGCTCTATCAAAACCCAACCACCTATGTTTCCGTTGGAACATCAACACTAAACCAGAGATTGGTACCAAAAATAGCCACCAGATCCAAAGTAAACGGGCAAAGTGGAAGGATGGAGTTCTTCTGGACAATTTTAAAACCGAATGATGCAATCAACTTCGAGAGTAATGGAAATTTCATTGCTCCAGAATATGCATACAAAATTGTCAAGAAAGGGGACTCAGCAATTATGAAAAGTGAATTGGAATATGGTAACTGCAATACCAAGTGTCAAACTCCAATGGGGGCGATAAACTCTAGTATGCCATTCCACAACATACACCCTCTCACCATCGGGGAATGCCCCAAATATGTGAAATCAAACAGATTAGTCCTTGCGACTGGGCTCAGAAATAGCCCTCAAAGAGAGAGAAGAAGAAAAAAGAGAGGACTATTTGGAGCTATAGCAGGTTTTATAGAGGGAGGATGGCAGGGAATGGTAGATGGTTGGTATGGATACCACCATAGCAATGAGCAGGGGAGTGGATACGCTGCAGACAAAGAATCCACTCAAAAGGCAATAGATGGAGTCACCAATAAGGTCAACTCGATCATTGACAAAATGAACACTCAGTTTGAGGCCGTTGGAAGGGAATTTAATAACTTAGAAAGGAGAATAGAGAATTTAAACAAGAAGATGGAAGACGGATTCCTAGATGTCTGGACTTATAATGCTGAACTTCTGGTTCTCATGGAAAATGAGAGAACTCTAGACTTTCATGACTCAAATGTCAAGAACCTTTACGACAAGGTCCGACTACAGCTTAGGGATAATGCAAAAGAGCTGGGTAACGGTTGTTTCGAGTTCTATCACAAATGTGATAATGAATGTATGGAAAGTGTAAGAAACGGAACGTATGACTACCCGCAGTATTCAGAAGAAGCAAGACTAAAAAGAGAGGAAATAAGTGGAGTAAAATTGGAATCAATAGGAACTTACCAAATACTGTCAATTTATTCAACAGTGGCGAGTTCCCTAGCGCTGGCAATCATGGTAGCTGGTCTATCTTTATGGATGTGCTCC------------------------
- 'TREESPARROW_HENAN_2_2004' ATGGAGAAAATAGTGCTTCTTCTTGCAATAGTCAGTCTTGTTAAAAGTGATCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACACAATAATGGAAAAGAACGTTACTGTTACACATGCTCAAGACATATTGGAAAAGACACACAACGGGAAGCTCTGCGACCTAGATGGAGTGAAGCCTCTAATTTTGAAAGATTGTAGTGTAGCTGGATGGCTCCTCGGAAACCCAATGTGTGACGAATTCATCAATGTGCCGGAGTGGTCTTACATAGTGGAGAAGGCCAGTCCAGCCAATGACCTCTGTTACCCAGGGGATTTCAACGACTATGAAGAACTGAAACACCTATTGAGCAGAATAAACCATTTTGAAAAAATTCAGATCATCCCCAAAAGTTCTTGGTCCGATCATGAAGCCTCATCAGGGGTGAGCTCAGCATGTCCATACCTGGGGAAGCCCTCCTTTTTCAGAAATGTGGTATGGCTTATCAAAAAGAACAGTACATACCCAACAATAAAGAGGGGCTACAATAATACCAACCAAGAAGATCTTTTGGTACTGTGGGGGATTCACCATCCTAATGATGCGGCAGAGCAGATAAAGCTCTATCAAAACCCAACCACCTATATTTCCGTTGGAACATCAACACTAAACCAGAGATTGGTACCAAAAATAGCTACTAGATCCAAAGTAAACGGACAAAGTGGAAGAATGGAGTTCTTCTGGACAATTTTAAAACCGAATGATGCTATCAATTTCGAGAGTAATGGAAATTTCATTGCTCCAGAATATGCATACAAAATTGTCAAGAAAGGGGACTCTGCAATTATGAAGAGTGAATTGGAATATGGCAACTGCAACACCAAGTGTCAAACTCCAGTGGGGGCGATAAATTCTAGCATGCCATTCCACAACATACACCCTCTCACCATCGGGGAATGCCCCAAATATGTGAAATCAAACAGATTAGTCCTTGCGACTGGACTCAGAAATGCCCCTCAAAGAGAGGGAAGAAGAAAAAAGAGAGGACTATTTGGAGCTATAGCAGGGTTTATAGAGGGAGGATGGCAGGGGATGGTAGATGGTTGGTATGGGTACCACCATAGCAATGAGCAGGGGAGTGGATACGCTGCAGACAAAGAATCCACTCAAAAAGCAATAGATGGAGTCACCAATAAGGTCAACTCGATCATTGACAAAATGAACACTCAGTTTGAGGCCGTTGGAAGGGAATTTAATAACTTAGAAAGGAGAATAGAAAATTTAAACAAGAAGATGGAGGACGGATTCCTAGATGTCTGGACTTATAATGCTGAACTTCTGGTTCTCATGGAAAATGAGAGAACTCTAGACTTTCATGACTCAAATGTCAAGAACCTTTACGAAAAGGTCCGACTACAACTTAGGGATAATGCAAAGGAGCTGGGTAACGGTTGTTTCGAGTTCTATCACAAATGTGATAATGAATGTATGGAAAGTGTAAAAAACGGAACGTATGACTACCGGCTGGACTCAGAAGAAGCAAGACTAAACAGAGAGGAAATAAGTGGAGTAAAATTGGAATCAATAGGAACTTACCAAATACTGTCAATTTATTCAACAGTGGCGAGTTCCCTAGCACTGGCAATCATGGTAGCTGGTCTATCTTTATGGATGTGCTCCAATGGATCGTTACAATGCAGAATT
- 'HONGKONG_538_97' ------------------------------------------------GATCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACACAATAATGGAAAAGAATGTTACTGTTACACATGCCCAAGACATACTGGAAAGGACACACAACGGGAAGCTCTGCGATCTAAATGGAGTGAAACCTCTCATTTTGAGGGATTGTAGTGTAGCTGGATGGCTCCTCGGAAACCCTATGTGTGACGAATTCATCAATGTGCCGGAATGGTCTTACATAGTGGAGAAGGCCAGTCCAGCCAATGACCTCTGTTATCCAGGGAATTTCAACGACTATGAAGAACTGAAACACCTATTGAGCAGAATAAACCATTTTGAGAAAATTCAGATCATCCCCAAAAGTTCTTGGTCCAATCATGATGCCTCATCAGGGGTGAGCTCAGCATGTCCATACCTTGGGAGGTCCTCCTTTTTCAGAAATGTGGTATGGCTTATCAAAAAGAACAGTGCATACCCAACAATAAAGAGGAGCTACAATAATACCAACCAAGAAGATCTTTTGGTACTGTGGGGGATTCACCATCCTAATGATGCGGCAGAGCAGACAAAGCTCTATCAAAATCCAACCACCTACATTTCCGTTGGAACATCAACACTGAACCAGAGATTGGTTCCAGAAATAGCTACTAGACCCAAAGTAAACGGGCAAAGTGGAAGAATGGAGTTCTTCTGGACAATTTTAAAGCCGAATGATGCCATCAATTTCGAGAGTAATGGAAATTTCATTGCCCCAGAATATGCATACAAAATTGTCAAGAAAGGGGACTCAACAATTATGAAAAGTGAATTGGAATATGGTAACTGCAACACCAAGTGTCAAACTCCAATGGGGGCGATAAACTCTAGTATGCCATTCCACAACATACACCCCCTCACCATCGGGGAATGCCCCAAATATGTGAAATCAAACAGATTAGTTCTTGCGACTGGACTCAGAAATACCCCTCAAAGGGAGAGAAGAAGAAAAAAGAGAGGACTATTTGGAGCTATAGCAGGTTTTATAGAGGGAGGATGGCAGGGAATGGTAGATGGTTGGTATGGGTACCACCATAGCAATGAGCAGGGGAGTGGATACGCTGCAGACCAAGAATCCACTCAAAAGGCAATAGATGGAGTCACCAATAAGGTCAACTCGATCATTAACAAAATGAACACTCAGTTTGAGGCCGTTGGAAGGGAATTTAATAACTTAGAAAGGAGAATAGAGAATTTAAACAAGAAAATGGAAGACGGATTCCTAGATGTCTGGACTTACAATGCTGAACTTCTGGTTCTCATGGAAAATGAGAGAACTCTCGACTTTCATGACTCAAATGTCAAGAACCTTTACGACAAGGTCCGACTACAGCTTAGGGATAATGCAAAGGAACTGGGTAATGGTTGTTTCGAATTCTATCACAAATGTGATAATGAATGTATGGAAAGTGTAAGAAACGGAACGTATGACTACCCGCAGTATTCAGAAGAAGCAAGACTAAACAGAGAGGAAATAAGTGGAGTAAAATTGGAATCAATGGGAACTTACCAAATACTGTCAATTTATTCAACAGTGGCGAGTTCCCTAGCACTGGCAATCATGGTAGCTGGTCTATCTTTATGGATGTGCTCCAATGGATCGTTACAATGCAGAATT;
+ 'DUCK_VIETNAM_272_2005' ATGGAGAAAATAGTGCTTCTTTTTGCAATAGTCAGTCTTGTTAAAAGTGATCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACACAATAATGGAAAAGAACGTTACTGTTACACATGCCCAAGACATACTGGAAAAGACACACAACGGGAAGCTCTGCGATCTAGATGGAGTGAAGCCTCTAATTTTGAGAGATTGTAGTGTAGCTGGATGGCTCCTTGGAAATCCAATGTGTGACGAATTCATCAATGTGCCGGAATGGTCTTACATAGTGGAGAAGGCCAATCCAGTCAATGACCTCTGTTACCCAGGGGATTTCAATGACTATGAAGAATTGAAACACCTATTGAGCAGAATAAACCATTTTGAGAAAATTCAGATCATCCCCAAAAGTTCTTGGCCCAGTCATGAAGCCTCATTAGGGGTGAGCTCAGCATGTCCATACCAGGGAAGGTCCTCCTTTTTCAGAAATGTGGTATGGCTTATCAAAAAGAACAGTACATATCCAACAATAAAGAGGAGCTACAATAATACCAACCAAGAAGATCTTTTGGTACTGTGGGGGATTCACCATCCTAATGATGCGGCAGAGCAGACAAAGCTCTATCAAAACCCAACCACCTATATTTCCGTTGGGACATCAACACTAAACCAGAGATTGATACCAAGAATAGCTACTAGATCCAAAGTAAACGGGCAAAGTGGAAGGATGGAGTTCTTCTGGACAATTTTAAAACCGAATGATGCAATCAATTTCGAGAGTAATGGAAATTTCATTGCCCCAGAATACGCATACAAAATTGTCAAGAAAGGGGACTCAACAATTATGAAAAGTGAATTGGAATATGGTAACTGCAACACCAAGTGTCAAACACCAATGGGGGCGATAAATTCTAGTATGCCATTCCACAATATACACCCTCTCACCATCGGGGAATGCCCCAAATATGTGAAATCAAACAGATTAGTCCTTGCGACTGGGCTCAGAAATAGCCCTCAAAGAGAGAGAAGA---AAAAAGAGAGGATTATTTGGAGCTATAGCAGGTTTTATAGAGGGGGGATGGCAGGGAATGGTAGATGGTTGGTATGGGTACCACCATAGCAATGAACAGGGGAGTGGGTACGCTGCAGACAAAGAATCCACTCAAAAGGCAATAGATGGAGTCACCAATAAGGTCAACTCGATCATTGACAAAATGAACACTCAGTTTGAGGCCGTTGGAAGGGAATTTAACAACTTAGAAAGGAGAATAGAGAATTTAAACAAGAAGATGGAAGACGGGTTCCTAGATGTCTGGACTTATAATGCTGAACTTCTGGTTCTCATGGAAAATGAGAGAACTCTAGACTTTCATGACTCAAATGTCAAGAACCTTTACGACAAGGTCCGACTACAGCTTAGGGATAATGCAAAGGAGCTGGGTAACGGTTGTTTCGAGTTCTATCATAAATGTGATAATGAATGTATGGAAAGTGTAAGAAATGGAACGTATGACTACCCGCAGTATTCAGAAGAAGCAAAACTAAAAAGAGAGGAAATAAGTGGAGTAAAATTGGAATCAATAGGAATTTACCAAATACTGTCAATTTATTCCACAGTAGCGAGTTCCCTAGCACTGGCAATCATGGTAGCTGGTCTATCCTTATGGATGTGCTCCAATGGGTCGTTACAATGCAGA---;
END;
-BEGIN HYPHY;
-
-
-global gard.overallModel.theta_AC:=0.1608961031892805;
-global gard.overallModel.theta_AG:=1;
-global gard.overallModel.theta_AT:=0.1352456564198792;
-global gard.overallModel.theta_CG:=0.04707636336428175;
-global gard.overallModel.theta_CT:=1.30079002451919;
-global gard.overallModel.theta_GT:=0.1450292160826765;
-gard.overallModel_Q={4,4};
-gard.overallModel_Q[0][0]:=0;
-gard.overallModel_Q[0][1]:=gard.overallModel.theta_AC*t;
-gard.overallModel_Q[0][2]:=gard.overallModel.theta_AG*t;
-gard.overallModel_Q[0][3]:=gard.overallModel.theta_AT*t;
-gard.overallModel_Q[1][0]:=gard.overallModel.theta_AC*t;
-gard.overallModel_Q[1][1]:=0;
-gard.overallModel_Q[1][2]:=gard.overallModel.theta_CG*t;
-gard.overallModel_Q[1][3]:=gard.overallModel.theta_CT*t;
-gard.overallModel_Q[2][0]:=gard.overallModel.theta_AG*t;
-gard.overallModel_Q[2][1]:=gard.overallModel.theta_CG*t;
-gard.overallModel_Q[2][2]:=0;
-gard.overallModel_Q[2][3]:=gard.overallModel.theta_GT*t;
-gard.overallModel_Q[3][0]:=gard.overallModel.theta_AT*t;
-gard.overallModel_Q[3][1]:=gard.overallModel.theta_CT*t;
-gard.overallModel_Q[3][2]:=gard.overallModel.theta_GT*t;
-gard.overallModel_Q[3][3]:=0;
-
-
-gard.overallModel_pi={
-{0.348155156102176}
-{0.1862618617585505}
-{0.2292365471173418}
-{0.2363464350219317}
-};
-Model gard.overallModel=(gard.overallModel_Q,gard.overallModel_pi);
-TRY_NUMERIC_SEQUENCE_MATCH=0;
-ACCEPT_ROOTED_TREES=0;
-
-UseModel (gard.overallModel);
-Tree gard.tree.part_0=(((((((TREESPARROW_HENAN_1_2004,TREESPARROW_HENAN_2_2004)Node6,CHICKEN_HEBEI_326_2005)Node5,SWINE_ANHUI_2004)Node4,((DUCK_GUANGZHOU_20_2005,(GOOSE_SHANTOU_2216_2005,PEREGRINEFALCON_HK_D0028_2004)Node14)Node12,CK_HK_WF157_2003)Node11)Node3,((TREESPARROW_HENAN_3_2004,((CHICKEN_HONGKONG_915_97,(HONGKONG_97_98,HONGKONG_538_97)Node24)Node22,(GOOSE_HONGKONG_W355_97,DUCK_HONGKONG_Y283_97)Node27)Node21)Node19,TREESPARROW_HENAN_4_2004)Node18)Node2,MALLARD_VIETNAM_16_2003)Node1,HUMAN_VIETNAM_CL105_2005,(((DUCK_VIETNAM_376_2005,CHICKEN_THAILAND_KANCHANABURI_CK_160_2005)Node35,VIETNAM_3062_2004)Node34,DUCK_VIETNAM_272_2005)Node33);
-
-UseModel (gard.overallModel);
-Tree gard.tree.part_1=((((((TREESPARROW_HENAN_1_2004,TREESPARROW_HENAN_3_2004)Node5,TREESPARROW_HENAN_2_2004)Node4,CHICKEN_HEBEI_326_2005)Node3,CK_HK_WF157_2003)Node2,((TREESPARROW_HENAN_4_2004,(((CHICKEN_HONGKONG_915_97,(GOOSE_HONGKONG_W355_97,DUCK_HONGKONG_Y283_97)Node18)Node16,HONGKONG_97_98)Node15,HONGKONG_538_97)Node14)Node12,((DUCK_GUANGZHOU_20_2005,GOOSE_SHANTOU_2216_2005)Node24,PEREGRINEFALCON_HK_D0028_2004)Node23)Node11)Node1,(SWINE_ANHUI_2004,DUCK_VIETNAM_272_2005)Node28,((HUMAN_VIETNAM_CL105_2005,DUCK_VIETNAM_376_2005)Node32,(VIETNAM_3062_2004,(MALLARD_VIETNAM_16_2003,CHICKEN_THAILAND_KANCHANABURI_CK_160_2005)Node37)Node35)Node31);
-
-UseModel (gard.overallModel);
-Tree gard.tree.part_2=(((((((TREESPARROW_HENAN_1_2004,TREESPARROW_HENAN_3_2004)Node6,TREESPARROW_HENAN_4_2004)Node5,((CHICKEN_HEBEI_326_2005,(SWINE_ANHUI_2004,TREESPARROW_HENAN_2_2004)Node13)Node11,((CHICKEN_HONGKONG_915_97,GOOSE_HONGKONG_W355_97)Node17,((DUCK_HONGKONG_Y283_97,HONGKONG_538_97)Node21,HONGKONG_97_98)Node20)Node16)Node10)Node4,(((DUCK_GUANGZHOU_20_2005,GOOSE_SHANTOU_2216_2005)Node27,PEREGRINEFALCON_HK_D0028_2004)Node26,CK_HK_WF157_2003)Node25)Node3,DUCK_VIETNAM_272_2005)Node2,CHICKEN_THAILAND_KANCHANABURI_CK_160_2005)Node1,((HUMAN_VIETNAM_CL105_2005,DUCK_VIETNAM_376_2005)Node35,MALLARD_VIETNAM_16_2003)Node34,VIETNAM_3062_2004);
-
-UseModel (gard.overallModel);
-Tree gard.tree.part_3=(TREESPARROW_HENAN_1_2004,((TREESPARROW_HENAN_3_2004,TREESPARROW_HENAN_4_2004)Node3,(CHICKEN_HEBEI_326_2005,(SWINE_ANHUI_2004,(((CHICKEN_HONGKONG_915_97,HONGKONG_97_98)Node12,(GOOSE_HONGKONG_W355_97,HONGKONG_538_97)Node15)Node11,((DUCK_HONGKONG_Y283_97,(((HUMAN_VIETNAM_CL105_2005,DUCK_VIETNAM_376_2005)Node23,(VIETNAM_3062_2004,MALLARD_VIETNAM_16_2003)Node26)Node22,(CHICKEN_THAILAND_KANCHANABURI_CK_160_2005,DUCK_VIETNAM_272_2005)Node29)Node21)Node19,(((DUCK_GUANGZHOU_20_2005,GOOSE_SHANTOU_2216_2005)Node34,PEREGRINEFALCON_HK_D0028_2004)Node33,CK_HK_WF157_2003)Node32)Node18)Node10)Node8)Node6)Node2,TREESPARROW_HENAN_2_2004);
-
-gard.tree.part_3.TREESPARROW_HENAN_1_2004.t=0;
-gard.tree.part_1.TREESPARROW_HENAN_1_2004.t=0;
-gard.tree.part_0.TREESPARROW_HENAN_1_2004.t=0.05857422297899689;
-gard.tree.part_2.TREESPARROW_HENAN_1_2004.t=0.005798111568087266;
-gard.tree.part_3.TREESPARROW_HENAN_3_2004.t=0.01695383083245294;
-gard.tree.part_2.TREESPARROW_HENAN_3_2004.t=0.01156150675123391;
-gard.tree.part_1.TREESPARROW_HENAN_3_2004.t=0.03158020592266798;
-gard.tree.part_0.TREESPARROW_HENAN_2_2004.t=0;
-gard.tree.part_2.Node6.t=0.005752114704153241;
-gard.tree.part_3.TREESPARROW_HENAN_4_2004.t=0;
-gard.tree.part_0.Node6.t=0.01958885448675768;
-gard.tree.part_1.Node5.t=0.01578562509096785;
-gard.tree.part_3.Node3.t=0.005626204820953347;
-gard.tree.part_1.TREESPARROW_HENAN_2_2004.t=0;
-gard.tree.part_2.TREESPARROW_HENAN_4_2004.t=0;
-gard.tree.part_0.CHICKEN_HEBEI_326_2005.t=0.08539581222205937;
-gard.tree.part_0.Node5.t=0.008785251348759461;
-gard.tree.part_1.Node4.t=0.01552365496180499;
-gard.tree.part_3.CHICKEN_HEBEI_326_2005.t=0.01695010846335837;
-gard.tree.part_2.Node5.t=0.01747850471818142;
-gard.tree.part_2.CHICKEN_HEBEI_326_2005.t=0.03503516761116889;
-gard.tree.part_0.SWINE_ANHUI_2004.t=0.03621095158276482;
-gard.tree.part_3.SWINE_ANHUI_2004.t=0.01691949144014183;
-gard.tree.part_1.CHICKEN_HEBEI_326_2005.t=0.1496461030392494;
-gard.tree.part_2.SWINE_ANHUI_2004.t=0;
-gard.tree.part_3.CHICKEN_HONGKONG_915_97.t=0;
-gard.tree.part_0.Node4.t=0.01276474575218522;
-gard.tree.part_1.Node3.t=0.01612849799536819;
-gard.tree.part_2.TREESPARROW_HENAN_2_2004.t=0.005755413025643006;
-gard.tree.part_3.HONGKONG_97_98.t=0;
-gard.tree.part_0.DUCK_GUANGZHOU_20_2005.t=0.0192766495791201;
-gard.tree.part_1.CK_HK_WF157_2003.t=0;
-gard.tree.part_1.Node2.t=0.01592666163239849;
-gard.tree.part_3.Node12.t=0.005624861726679271;
-gard.tree.part_2.Node13.t=0.04104583433145084;
-gard.tree.part_0.GOOSE_SHANTOU_2216_2005.t=0.02571681083120876;
-gard.tree.part_3.GOOSE_HONGKONG_W355_97.t=0;
-gard.tree.part_2.Node11.t=0.02959620214340473;
-gard.tree.part_0.PEREGRINEFALCON_HK_D0028_2004.t=0.01927228350389201;
-gard.tree.part_1.TREESPARROW_HENAN_4_2004.t=0.01603326337757626;
-gard.tree.part_0.Node14.t=0;
-gard.tree.part_2.CHICKEN_HONGKONG_915_97.t=0;
-gard.tree.part_3.HONGKONG_538_97.t=0;
-gard.tree.part_1.CHICKEN_HONGKONG_915_97.t=0;
-gard.tree.part_3.Node15.t=0;
-gard.tree.part_2.GOOSE_HONGKONG_W355_97.t=0;
-gard.tree.part_1.GOOSE_HONGKONG_W355_97.t=0;
-gard.tree.part_0.Node12.t=0.01937459125256855;
-gard.tree.part_3.Node11.t=0.04554209130172088;
-gard.tree.part_2.Node17.t=0.005762026237197876;
-gard.tree.part_0.CK_HK_WF157_2003.t=0.02596326262653399;
-gard.tree.part_1.DUCK_HONGKONG_Y283_97.t=0;
-gard.tree.part_3.DUCK_HONGKONG_Y283_97.t=0.0005759546239426398;
-gard.tree.part_0.Node11.t=0.01934041428249825;
-gard.tree.part_2.DUCK_HONGKONG_Y283_97.t=0;
-gard.tree.part_1.Node18.t=0.01573819763328357;
-gard.tree.part_2.HONGKONG_538_97.t=0;
-gard.tree.part_0.Node3.t=0.01296660016108598;
-gard.tree.part_3.HUMAN_VIETNAM_CL105_2005.t=0.005721407160363217;
-gard.tree.part_1.Node16.t=0;
-gard.tree.part_3.DUCK_VIETNAM_376_2005.t=0.01134934181938971;
-gard.tree.part_2.Node21.t=0;
-gard.tree.part_1.HONGKONG_97_98.t=0;
-gard.tree.part_0.TREESPARROW_HENAN_3_2004.t=0.01279117837719664;
-gard.tree.part_3.Node23.t=0.005639505533994093;
-gard.tree.part_2.HONGKONG_97_98.t=0.01733030189067928;
-gard.tree.part_0.CHICKEN_HONGKONG_915_97.t=0;
-gard.tree.part_1.Node15.t=0;
-gard.tree.part_2.Node20.t=0.005764601606851516;
-gard.tree.part_3.VIETNAM_3062_2004.t=0.005771733097152759;
-gard.tree.part_0.HONGKONG_97_98.t=0.02146751702093312;
-gard.tree.part_1.HONGKONG_538_97.t=0;
-gard.tree.part_2.Node16.t=0.05897334149573956;
-gard.tree.part_3.MALLARD_VIETNAM_16_2003.t=0;
-gard.tree.part_1.Node14.t=0.04761029025363051;
-gard.tree.part_0.HONGKONG_538_97.t=0;
-gard.tree.part_3.Node26.t=0;
-gard.tree.part_1.Node12.t=0.03161896192027676;
-gard.tree.part_0.Node24.t=0;
-gard.tree.part_2.Node10.t=0.01754811725473135;
-gard.tree.part_0.Node22.t=0;
-gard.tree.part_2.Node4.t=0.01746770341506559;
-gard.tree.part_3.Node22.t=0;
-gard.tree.part_1.DUCK_GUANGZHOU_20_2005.t=0.06399313768340011;
-gard.tree.part_3.CHICKEN_THAILAND_KANCHANABURI_CK_160_2005.t=0.01130019595897338;
-gard.tree.part_2.DUCK_GUANGZHOU_20_2005.t=0.01155345754532932;
-gard.tree.part_0.GOOSE_HONGKONG_W355_97.t=0;
-gard.tree.part_1.GOOSE_SHANTOU_2216_2005.t=0.01577339102928018;
-gard.tree.part_1.Node24.t=0;
-gard.tree.part_3.DUCK_VIETNAM_272_2005.t=0.01705943197980908;
-gard.tree.part_0.DUCK_HONGKONG_Y283_97.t=0;
-gard.tree.part_2.GOOSE_SHANTOU_2216_2005.t=0.01158856502947429;
-gard.tree.part_3.Node29.t=0.005591340030380314;
-gard.tree.part_0.Node27.t=0.006409970581946693;
-gard.tree.part_1.PEREGRINEFALCON_HK_D0028_2004.t=0.01575671036454394;
-gard.tree.part_2.Node27.t=0.005762269220625183;
-gard.tree.part_2.PEREGRINEFALCON_HK_D0028_2004.t=0.01156958073466321;
-gard.tree.part_3.Node21.t=0.01820789791069541;
-gard.tree.part_0.Node21.t=0.07868188555962134;
-gard.tree.part_1.Node23.t=0;
-gard.tree.part_3.Node19.t=0.02064116615940968;
-gard.tree.part_1.Node11.t=0.01579982248808471;
-gard.tree.part_2.Node26.t=0.005790936241909173;
-gard.tree.part_0.Node19.t=0.006556136739028721;
-gard.tree.part_2.CK_HK_WF157_2003.t=0.01740104634041944;
-gard.tree.part_3.DUCK_GUANGZHOU_20_2005.t=0.01122269526273182;
-gard.tree.part_1.Node1.t=0.03191609280002815;
-gard.tree.part_0.TREESPARROW_HENAN_4_2004.t=0.02583732273754462;
-gard.tree.part_3.GOOSE_SHANTOU_2216_2005.t=0.01704950698467438;
-gard.tree.part_0.Node18.t=0;
-gard.tree.part_1.SWINE_ANHUI_2004.t=0.04786067821076487;
-gard.tree.part_2.Node25.t=0.005714353746749828;
-gard.tree.part_3.Node34.t=0.01699932637509961;
-gard.tree.part_2.Node3.t=0.02909111290817361;
-gard.tree.part_1.DUCK_VIETNAM_272_2005.t=0.01582432262534449;
-gard.tree.part_0.Node2.t=0.04531535142849069;
-gard.tree.part_3.PEREGRINEFALCON_HK_D0028_2004.t=0;
-gard.tree.part_2.DUCK_VIETNAM_272_2005.t=0.04688786037187378;
-gard.tree.part_1.Node28.t=0.01585428836641066;
-gard.tree.part_0.MALLARD_VIETNAM_16_2003.t=0.006418275987313576;
-gard.tree.part_2.Node2.t=0;
-gard.tree.part_0.Node1.t=0;
-gard.tree.part_1.HUMAN_VIETNAM_CL105_2005.t=0.04793987394516301;
-gard.tree.part_3.Node33.t=0.005588817804782144;
-gard.tree.part_2.CHICKEN_THAILAND_KANCHANABURI_CK_160_2005.t=0.01154453879187037;
-gard.tree.part_3.CK_HK_WF157_2003.t=0.01716258181594375;
-gard.tree.part_1.DUCK_VIETNAM_376_2005.t=0.04814712785088576;
-gard.tree.part_0.HUMAN_VIETNAM_CL105_2005.t=0.03233261944427364;
-gard.tree.part_3.Node32.t=0.01093952353546261;
-gard.tree.part_1.Node32.t=0.01603439924229737;
-gard.tree.part_2.Node1.t=0;
-gard.tree.part_0.DUCK_VIETNAM_376_2005.t=0.006426405166263041;
-gard.tree.part_3.Node18.t=0.006999924576403242;
-gard.tree.part_2.HUMAN_VIETNAM_CL105_2005.t=0.01158837432608151;
-gard.tree.part_1.VIETNAM_3062_2004.t=0;
-gard.tree.part_0.CHICKEN_THAILAND_KANCHANABURI_CK_160_2005.t=0.03243143023600951;
-gard.tree.part_2.DUCK_VIETNAM_376_2005.t=0.04084931774911551;
-gard.tree.part_0.Node35.t=0.006425881940410614;
-gard.tree.part_3.Node10.t=0.01122126625283681;
-gard.tree.part_1.MALLARD_VIETNAM_16_2003.t=0.03164618061938185;
-gard.tree.part_3.Node8.t=0.01138375571529405;
-gard.tree.part_1.CHICKEN_THAILAND_KANCHANABURI_CK_160_2005.t=0;
-gard.tree.part_0.VIETNAM_3062_2004.t=0;
-gard.tree.part_2.Node35.t=0.005735380080537774;
-gard.tree.part_2.MALLARD_VIETNAM_16_2003.t=0.01153522589478997;
-gard.tree.part_0.Node34.t=0.006411307059451499;
-gard.tree.part_3.Node6.t=0.005620575706477796;
-gard.tree.part_1.Node37.t=0.01577522590128735;
-gard.tree.part_2.Node34.t=0;
-gard.tree.part_1.Node35.t=0;
-gard.tree.part_3.Node2.t=0;
-gard.tree.part_0.DUCK_VIETNAM_272_2005.t=0.01929221555619922;
-gard.tree.part_3.TREESPARROW_HENAN_2_2004.t=0.02277373031525211;
-gard.tree.part_0.Node33.t=0;
-gard.tree.part_2.VIETNAM_3062_2004.t=0.005759594754296721;
-gard.tree.part_1.Node31.t=0;
-DataSet gard.sequences = ReadDataFile(USE_NEXUS_FILE_DATA);
-DataSetFilter gard.filter.part_0 = CreateFilter(gard.sequences,1,"0-461","0,19,3,13,11,16,18,12,17,4,15,20,6,7,2,9,1,8,10,5,14");
-DataSetFilter gard.filter.part_1 = CreateFilter(gard.sequences,1,"462-650","0,17,19,3,12,2,4,6,7,15,20,11,16,18,13,14,1,8,5,9,10");
-DataSetFilter gard.filter.part_2 = CreateFilter(gard.sequences,1,"651-1166","0,17,2,3,13,19,4,6,7,20,15,11,16,18,12,14,10,1,8,9,5");
-DataSetFilter gard.filter.part_3 = CreateFilter(gard.sequences,1,"1167-1697","0,17,2,3,13,4,15,6,20,7,1,8,5,9,10,14,11,16,18,12,19");
-ASSUME_REVERSIBLE_MODELS=0;
-LikelihoodFunction DJoxWylN.likelihoodFunction = (gard.filter.part_0,gard.tree.part_0,gard.filter.part_1,gard.tree.part_1,gard.filter.part_2,gard.tree.part_2,gard.filter.part_3,gard.tree.part_3);
-
-END;
\ No newline at end of file
+BEGIN ASSUMPTIONS;
+ CHARSET span_1 = 1-697;
+ CHARSET span_2 = 698-1167;
+ CHARSET span_3 = 1168-1698;
+END;
+BEGIN TREES;
+ TREE tree_1 = ((((((((TREESPARROW_HENAN_1_2004:0.0145769244137292,TREESPARROW_HENAN_2_2004:1e-10)Node7:0.005925131124384257,CHICKEN_HEBEI_326_2005:0.03148335967389677)Node6:0.006520820816328921,((DUCK_GUANGZHOU_20_2005:0.009483822383439561,(GOOSE_SHANTOU_2216_2005:0.007374093130581441,PEREGRINEFALCON_HK_D0028_2004:0.007242107381463219)Node14:0.0007056004954733679)Node12:0.00710363602212726,CK_HK_WF157_2003:0.00757594740908166)Node11:0.004227199989057285)Node5:0.001170889307235767,TREESPARROW_HENAN_3_2004:0.008919169512223372)Node4:0.0008380584919822353,(TREESPARROW_HENAN_4_2004:0.006708184198226799,((CHICKEN_HONGKONG_915_97:1e-10,(HONGKONG_97_98:0.006483231977175029,HONGKONG_538_97:1e-10)Node24:0.0003031375872603963)Node22:0.0001037022453470389,(GOOSE_HONGKONG_W355_97:1e-10,DUCK_HONGKONG_Y283_97:1e-10)Node27:0.002891685438446985)Node21:0.02744187404194088)Node19:0.002944759819938243)Node3:0.001672904530995233,SWINE_ANHUI_2004:0.01260983958335299)Node2:0.01303612329048956,DUCK_VIETNAM_272_2005:0.008088746451854261)Node1:0.0006545914783555439,((HUMAN_VIETNAM_CL105_2005:0.01105269263722943,DUCK_VIETNAM_376_2005:0.006417734235732284)Node33:0.002021990910251294,VIETNAM_3062_2004:0.002304874937323682)Node32:0.0006817702832121299,(MALLARD_VIETNAM_16_2003:0.005709114871229771,CHICKEN_THAILAND_KANCHANABURI_CK_160_2005:0.008864540916547606)Node37:9.336374870077841e-05);
+ TREE tree_2 = ((((((TREESPARROW_HENAN_1_2004:0.002586740118529802,TREESPARROW_HENAN_3_2004:0.003828953390398881)Node5:0.00187457851284572,TREESPARROW_HENAN_4_2004:0.0002656521581222459)Node4:0.008299727091877812,((CHICKEN_HEBEI_326_2005:0.01484958179784225,(SWINE_ANHUI_2004:1e-10,TREESPARROW_HENAN_2_2004:0.002239639293515125)Node12:0.01361271232984685)Node10:0.01278549184522065,((CHICKEN_HONGKONG_915_97:1e-10,GOOSE_HONGKONG_W355_97:1e-10)Node16:0.001326679361120118,((DUCK_HONGKONG_Y283_97:0.0006676977779578139,HONGKONG_538_97:1e-10)Node20:0.0006271503105586317,HONGKONG_97_98:0.004109899012531796)Node19:0.001653355437332724)Node15:0.01224714418221361)Node9:0.003429034672045344)Node3:0.005031763140085913,(((DUCK_GUANGZHOU_20_2005:0.004262245747717084,GOOSE_SHANTOU_2216_2005:0.004308213533754201)Node26:0.002157320455556664,CK_HK_WF157_2003:0.00647028357035998)Node25:4.000752717957338e-05,PEREGRINEFALCON_HK_D0028_2004:0.002090471815463569)Node24:0.003260422306103818)Node2:0.00707214212698231,DUCK_VIETNAM_272_2005:0.01454290899825338)Node1:0.0007147389821184919,(((HUMAN_VIETNAM_CL105_2005:0.004710041013757377,DUCK_VIETNAM_376_2005:0.01496207542884359)Node34:0.001166828623060772,MALLARD_VIETNAM_16_2003:0.003061545152147631)Node33:0.001134022328667363,VIETNAM_3062_2004:1e-10)Node32:0.0002767006572468676,CHICKEN_THAILAND_KANCHANABURI_CK_160_2005:0.00405819047265216);
+ TREE tree_3 = (TREESPARROW_HENAN_1_2004:1.793736422068138e-05,((TREESPARROW_HENAN_3_2004:0.005512611253559831,TREESPARROW_HENAN_4_2004:0.000171467489882283)Node3:0.001655366533442949,(CHICKEN_HEBEI_326_2005:0.005483900345571787,(SWINE_ANHUI_2004:0.006320038544899231,(((CHICKEN_HONGKONG_915_97:1e-10,HONGKONG_97_98:1e-10)Node12:0.001309621960005619,(GOOSE_HONGKONG_W355_97:1e-10,HONGKONG_538_97:1e-10)Node15:0.0005799496924062597)Node11:0.01406566295495963,((DUCK_HONGKONG_Y283_97:999.9836725287659,(((HUMAN_VIETNAM_CL105_2005:0.002027831968935447,DUCK_VIETNAM_376_2005:0.003754856650868615)Node23:0.00177604858958343,(VIETNAM_3062_2004:0.002068037509299944,MALLARD_VIETNAM_16_2003:1e-10)Node26:0.0001623690336813484)Node22:0.0008290773242978894,(CHICKEN_THAILAND_KANCHANABURI_CK_160_2005:0.004523465945045592,DUCK_VIETNAM_272_2005:0.005056282226890766)Node29:0.001128740164377167)Node21:0.01150309854222087)Node19:0.001994389759866116,(((DUCK_GUANGZHOU_20_2005:0.003847909099661096,GOOSE_SHANTOU_2216_2005:0.005686200296849465)Node34:0.006130725555048717,PEREGRINEFALCON_HK_D0028_2004:8.387427766777967e-05)Node33:0.0009906361822363255,CK_HK_WF157_2003:0.005714641337818262)Node32:0.004952071733007253)Node18:0.002028752021615747)Node10:0.004186888950236505)Node8:0.002350770416932014)Node6:0.002154523112988181)Node2:0.0002651492563879275,TREESPARROW_HENAN_2_2004:0.007562549920247083);
+END;