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Commit f3510ac0 authored by Birgitta Paeuker's avatar Birgitta Paeuker
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Added the TreeCmp source code

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((a,f),(b,(c,(d,e))));
((a,e),((b,f),(c,d)));
No Tree1 Tree2 MatchingCluster
1 1 2 7.0000
---------
Summary:
Name Avg Std Min Max Count
MatchingCluster 7.0 0.0 7.0 7.0 1
Alignemnt: 1
Tree1: 1
Tree2: 2
Alignemnt cost (distance): 7
Aligned clusters:
1. (a, f) <-> (b, f)
Cost: 2
2. (d, e) <-> (a, e)
Cost: 2
3. (c, d, e) <-> (c, d)
Cost: 1
4. (b, c, d, e) <-> (b, c, d, f)
Cost: 2
-----------------
1)
java -jar TreeCmp.jar -w 2 -d mc -i align.trees -o align.trees.out -I -A
1)
java -jar TreeCmp.jar -w 2 -d ms -i testBSP.newick -o testBSP.newick_w_2.out -I
2)
java -jar TreeCmp.jar -w 3 -d ms -i testBSP.newick -o testBSP.newick_w_3.out -I
3)
java -jar TreeCmp.jar -s -d ms rf -i testBSP.newick -o testBSP.newick_s.out -N
4)
java -jar TreeCmp.jar -m -d ms rf qt -i testBSP.newick -o testBSP.newick_m.out
5)
java -jar TreeCmp.jar -m -d ms rf qt pd -i testBSP.nexus -o testBSP.nexus_m.out
tree STATE_0 = [&R] (((1:7.158048931427864,(((2:15.780648580883451,(17:13.508824186664437,(((6:2.3026652379284016,7:3.3026652379284016):5.895962839130295,3:8.198628077058697):9.870342140220469,8:28.068970217279166):1.4398539693852719):4.2718243942190135):2.9609038793952323,9:19.741552460278683):0.21780686085917011,10:26.959359321137853):8.19868961029001):30.83060976864737,(4:43.31259768133317,5:44.31259768133317):20.67606101874206):62.575906863775685,((15:27.468897900644706,16:9.468897900644706):76.36271969662677,(11:7.871339468838961,((12:0.8742463587729006,14:8.8742463587729):0.15998273324675694,13:2.0342290920196575):20.837110376819304):78.96027812843252):21.732947966579445);
tree STATE_1000 = [&R] (((14:46.54134840609228,11:24.541348406092283):19.65730936598561,((((2:5.824602467185969E-4,9:1.0005824602467186):0.0026946431216536837,((13:0.020233456138937456,(3:2.660190065027683,(((5:0.06148616908878424,7:2.0614861690887842):0.9449245869045466,4:0.006410755993330852):0.06825416366764969,10:2.0746649196609805):0.5855251453667023):2.3600433911112546):1.0308056513589658,(12:0.032450133358970845,17:0.032450133358970845):0.018588974138932457):1.952237995870469):4.600125986932309,((15:0.012878228199886266,6:3.0128782281998863):1.4597918020491392,8:14.472670030249025):8.130733060051655):42.18343188622985,16:33.78683497653053):9.411822795547366):30.51581245210356,1:66.71447022418145);
tree STATE_2000 = [&R] ((((2:1.773968332942946,(6:9.374186801935679,((13:0.18383252981468345,((15:0.06991341795042949,((14:3.394167902325121,5:0.3941679023251208):1.0784226369883605,((8:10.931753154990842,10:0.931753154990842):1.306734190921322,4:0.23848734591216392):0.23410319340131736):0.5973228786369482):0.3237137952534237,7:4.393627213203853):1.7902053166108303):2.344657544848456,9:0.5284900746631394):1.8456967272725393):0.39978153100726743):6.925972705132384,(12:3.5757153057340787,(3:8.194870778130142,17:2.1948707781301415):1.3808445276039372):7.124225732341252):12.776660887466406,(11:8.550270611063084,1:0.550270611063084):0.9263313144786522):1.0240584074850432,16:9.50066033302678);
tree STATE_3000 = [&R] ((((((8:15.36517952798215,(15:5.380816623485885E-4,(4:0.9670220446635902,(5:1.3485622063552167,10:2.3485622063552167):0.6184598383083735):0.03351603699875838):2.3646414463198013):1.9153753701026233,((14:8.17122766895249,7:7.17122766895249):0.8532369929584291,13:2.024464661910919):0.2560902361738542):2.5588590904286015,9:2.8394139885133747):0.6525881730562908,2:2.4920021615696655):41.68475294741461,((6:33.25411818122345,(11:12.90626623715955,1:4.906266237159549):0.34785194406389763):17.85459566469381,((3:10.10098506637247,12:4.10098506637247):9.383285525862352,17:13.484270592234822):31.624443253682436):1.0680412630670162):11.352466246937574,16:42.52922135592185);
tree STATE_4000 = [&R] (((((((14:6.859926025588402,7:5.859926025588402):1.381986893682976,(8:15.05705537365652,(15:0.005332039743800365,(4:0.9515317987195129,(5:1.4436815143806108,10:2.4436815143806108):0.5078502843389021):0.05380024102428749):2.0517233339127188):1.1848575456148591):0.42754207187800475,13:1.669454991149383):3.628333269425063,9:3.297788260574446):1.3333493740901403,2:3.6311376346645865):30.510416249269436,(((6:21.80215224009635,11:1.8021522400963512):6.921409353085391,1:0.7235615931817421):11.00387418675875,((3:14.823558868898274,12:8.823558868898274):11.609836602426157,17:20.43339547132443):13.294040308616061):2.4141181039935304):8.934837925629324,16:30.076391809563347);
tree STATE_5000 = [&R] ((((((13:1.6734561953835403,7:7.67345619538354):0.743400444258544,((14:6.204684122006901,((10:3.049818986942485,4:1.0498189869424852):0.2463288912092505,(15:0.28987060111028384,5:2.289870601110284):0.0062772770414518675):0.9085362438551652):0.039648032215923834,8:14.244332154222825):3.1725244854192596):4.061647122509992,2:3.4785037621520765):1.3344319671373093,9:5.812935729289386):43.38983919327553,(((6:21.99908571694836,11:1.9990857169483611):9.846201904816116,1:3.845287621764477):11.666820437868942,((3:10.412603565241167,12:4.412603565241167):13.560115779605947,17:17.972719344847114):19.539388714786305):12.690666862931494):1.5478407200656505,16:36.750615642630564);
tree STATE_6000 = [&R] ((((((13:1.0333805329311012,((((4:1.5627175352590648,10:3.5627175352590648):0.031292972804735086,(15:0.5476244459397392,5:2.5476244459397392):0.0463860621240606):1.1035859966677926,8:14.697596504731592):0.7097035162087106,14:7.407300020940303):0.6260805119907982):0.41203471344480036,7:7.445415246375902):3.760978802693046,2:2.2063940490689475):0.43480344506795987,9:3.6411974941369074):30.87738962621611,(((6:22.301693283613183,11:2.301693283613183):9.026536652182855,1:3.3282299357960383):6.467045734385451,((3:9.783646223397852,12:3.7836462233978523):15.244706832791678,17:19.02835305618953):12.766922613991959):3.723311450171529):11.248101259165011,16:31.76668837951803);
tree STATE_7000 = [&R] ((((((13:1.4789330647842291,7:7.478933064784229):0.22086572720810338,((((15:0.4709483172425397,5:2.4709483172425397):0.048792868200459694,(4:0.8366342068741428,8:12.836634206874143):0.6831069785688566):0.40571564382210745,10:3.925456829265107):0.7086904154611222,14:6.634147244726229):2.0656515472661034):3.6813015416521964,9:3.381100333644529):0.7236458140845272,2:3.104746147729056):35.49104967293272,(((6:23.499534187112936,11:3.4995341871129355):6.28054469398635,1:1.7800788810992856):9.257503891529389,((3:10.250530963633793,12:4.250530963633793):13.873411646650375,17:18.123942610284168):14.913640162344507):7.558213048033096):7.147376660779457,16:32.74317248144123);
tree STATE_8000 = [&R] ((((9:3.9820104678808157,2:2.9820104678808157):0.3440533957859735,((((8:15.22959697985274,14:7.22959697985274):0.008124472100789148,((15:0.4149442029932171,10:3.414944202993217):0.8258166627049803,(5:2.6491402961242603,4:1.6491402961242603):0.5916205695739372):0.9969605862553319):1.5479887664368022,13:1.7857102183903315):0.11615420756072226,7:7.901864425951054):4.424199437715735):35.3364894734205,(((6:22.490207819083082,11:2.490207819083082):7.42976909774611,1:1.9199769168291922):9.163534806163597,((3:12.774418755363811,12:6.774418755363811):10.267216818811043,17:17.041635574174855):16.041876148817934):7.5790416140945):6.645153042852918,16:32.30770637994021);
tree STATE_9000 = [&R] (((((((8:14.44491118748396,((10:2.8895058872156696,4:0.8895058872156696):0.46562630054386034,(15:0.21990116666887083,5:2.219901166668871):0.1352310210906591):1.0897789997244303):1.1778132864634099,(7:6.101238589115887,14:7.101238589115887):0.521485884831483):0.2460889325188429,13:0.868813406466213):4.765071704453252,9:3.633885110919465):0.9364900581142734,2:3.5703751690337384):29.60204879609428,(((6:23.499753551023325,11:3.499753551023325):8.32650712168875,1:3.826260672712074):6.063499524087256,((3:11.027841462691548,12:5.027841462691548):7.901252235063886,17:12.929093697755434):18.960666499043896):3.282663768328689):8.221910802128939,16:28.394334767256957);
tree STATE_10000 = [&R] ((((((7:7.298927374846272,((8:14.594449630582348,(((5:1.8183725864769062,10:2.8183725864769062):1.1928901757298593,15:1.0112627622067656):0.2510420661407231,4:2.2623048283474887):0.3321448022348594):0.6052171029262272,14:7.199666733508575):1.0992606413376969):0.21621677291872032,13:1.5151441477649925):4.061546791702426,9:3.5766909394674187):1.6690945638107024,2:4.245785503278121):41.552931060074904,(((6:23.690742294247336,11:3.690742294247336):8.892634669632024,1:4.58337696387936):8.566344789621937,((3:10.696748632586399,12:4.696748632586399):12.737683436267972,17:17.43443206885437):17.715289684646926):12.648994809851729):5.417969764104868,16:38.21668632745789);
End;
No Tree1 Tree2 MatchingSplit R-F Quartet
1 1 2 58.0000 14.0000 1561.0000
2 1 3 68.0000 14.0000 1633.0000
3 1 4 62.0000 14.0000 1632.0000
4 1 5 66.0000 14.0000 1661.0000
5 1 6 64.0000 14.0000 1663.0000
6 1 7 67.0000 14.0000 1643.0000
7 1 8 62.0000 14.0000 1682.0000
8 1 9 61.0000 13.0000 1622.0000
9 1 10 65.0000 14.0000 1671.0000
10 1 11 68.0000 14.0000 1655.0000
11 2 3 54.0000 14.0000 1429.0000
12 2 4 48.0000 14.0000 1434.0000
13 2 5 48.0000 14.0000 1431.0000
14 2 6 50.0000 14.0000 1463.0000
15 2 7 54.0000 14.0000 1468.0000
16 2 8 50.0000 14.0000 1469.0000
17 2 9 45.0000 13.0000 1395.0000
18 2 10 49.0000 14.0000 1454.0000
19 2 11 52.0000 14.0000 1444.0000
20 3 4 24.0000 10.0000 552.0000
21 3 5 20.0000 10.0000 476.0000
22 3 6 24.0000 11.0000 554.0000
23 3 7 23.0000 11.0000 543.0000
24 3 8 22.0000 10.0000 487.0000
25 3 9 27.0000 11.0000 568.0000
26 3 10 21.0000 10.0000 483.0000
27 3 11 20.0000 9.0000 448.0000
28 4 5 8.0000 2.0000 104.0000
29 4 6 14.0000 7.0000 258.0000
30 4 7 19.0000 6.0000 259.0000
31 4 8 14.0000 6.0000 230.0000
32 4 9 15.0000 7.0000 303.0000
33 4 10 11.0000 4.0000 144.0000
34 4 11 16.0000 4.0000 180.0000
35 5 6 10.0000 6.0000 244.0000
36 5 7 13.0000 5.0000 200.0000
37 5 8 10.0000 5.0000 216.0000
38 5 9 13.0000 6.0000 244.0000
39 5 10 3.0000 2.0000 40.0000
40 5 11 8.0000 2.0000 76.0000
41 6 7 9.0000 2.0000 98.0000
42 6 8 8.0000 4.0000 186.0000
43 6 9 15.0000 5.0000 207.0000
44 6 10 7.0000 4.0000 204.0000
45 6 11 12.0000 5.0000 194.0000
46 7 8 13.0000 4.0000 196.0000
47 7 9 16.0000 4.0000 153.0000
48 7 10 10.0000 3.0000 160.0000
49 7 11 7.0000 4.0000 150.0000
50 8 9 13.0000 6.0000 254.0000
51 8 10 7.0000 4.0000 190.0000
52 8 11 12.0000 4.0000 152.0000
53 9 10 14.0000 6.0000 257.0000
54 9 11 15.0000 5.0000 194.0000
55 10 11 9.0000 3.0000 90.0000
No Tree1 Tree2 MatchingSplit MatchingSplit_toYuleAvg MatchingSplit_toUnifAvg R-F R-F_toYuleAvg R-F_toUnifAvg
1 1 2 58.0000 1.1425 1.0114 14.0000 1.0180 1.0130
2 2 3 54.0000 1.0637 0.9417 14.0000 1.0180 1.0130
3 3 4 24.0000 0.4728 0.4185 10.0000 0.7271 0.7235
4 4 5 8.0000 0.1576 0.1395 2.0000 0.1454 0.1447
5 5 6 10.0000 0.1970 0.1744 6.0000 0.4363 0.4341
6 6 7 9.0000 0.1773 0.1569 2.0000 0.1454 0.1447
7 7 8 13.0000 0.2561 0.2267 4.0000 0.2908 0.2894
8 8 9 13.0000 0.2561 0.2267 6.0000 0.4363 0.4341
9 9 10 14.0000 0.2758 0.2441 6.0000 0.4363 0.4341
10 10 11 9.0000 0.1773 0.1569 3.0000 0.2181 0.2171
No Tree1 Tree2 MatchingSplit
1 1 2 58.0000
2 3 4 24.0000
3 5 6 10.0000
4 7 8 13.0000
5 9 10 14.0000
---------
Summary:
Name Avg Std Min Max Count
MatchingSplit 23.8 17.73583942191629 10.0 58.0 5
No Tree1 Tree2 MatchingSplit
1 1 2 58.0000
2 1 3 68.0000
3 2 3 54.0000
4 4 5 8.0000
5 4 6 14.0000
6 5 6 10.0000
7 7 8 13.0000
8 7 9 16.0000
9 8 9 13.0000
10 10 11 9.0000
---------
Summary:
Name Avg Std Min Max Count
MatchingSplit 26.3 22.410042391749286 8.0 68.0 10
#NEXUS
Begin taxa;
Dimensions ntax=17;
Taxlabels
D4ElSal94
D4Tahiti85
D4Philip84
D4ElSal83
D4Tahiti79
D4Thai63
D4NewCal81
D4Thai84
D4Brazi82
D4Thai78
D4Indon77
D4Philip64
D4SLanka78
D4Indon76
D4Mexico84
D4Philip56
D4PRico86
;
End;
Begin trees;
Translate
1 D4ElSal94,
2 D4Tahiti85,
3 D4Philip84,
4 D4ElSal83,
5 D4Tahiti79,
6 D4Thai63,
7 D4NewCal81,
8 D4Thai84,
9 D4Brazi82,
10 D4Thai78,
11 D4Indon77,
12 D4Philip64,
13 D4SLanka78,
14 D4Indon76,
15 D4Mexico84,
16 D4Philip56,
17 D4PRico86
;
tree STATE_0 = [&R] (((12:18.81681608921457,13:32.81681608921457):20.21304292887588,((9:11.535545910724217,(10:4.243848280017822,11:3.243848280017822):3.2916976307063948):19.89210065798543,15:33.42764656870965):25.6022124493808):95.9259117198303,(((5:25.27131565595589,(7:24.507199715852032,(8:9.61265001525992,14:1.61265001525992):17.894549700592112):2.7641159401038564):56.79721281576904,((3:10.308282964877733,4:9.308282964877733):63.01351593325164,((1:20.52977975479703,2:11.52977975479703):24.274817132027646,6:13.804596886824676):38.5172020113047):13.746729573595559):21.784032037488828,(16:21.567045213612538,17:51.56704521361254):59.28551529560122):46.103210228706985);
tree STATE_1000 = [&R] ((1:46.017353888817766,((5:0.21452213913075724,7:2.2145221391307572):26.14976823540595,(14:20.402298687244276,((17:13.380091863726456,(((2:3.6816382422593463,9:0.6816382422593463):1.084164451960099,15:3.7658026942194454):3.36423422114769,4:6.1300369153671355):4.25005494835932):8.06040361983747,11:12.440495483563925):8.96180320368035):2.961991687292432):4.653063514281058):26.078977315857372,(6:16.4148502845336,((13:7.486595137921896,10:7.486595137921896):23.785968950412347,(12:14.965887624139874,(3:33.50013133490667,(8:32.85710444384522,16:4.857104443845223):0.6430268910614458):1.4657562892332052):2.306676464194368):0.14228619619935756):24.68148092014154);
tree STATE_2000 = [&R] (((14:15.68035129161531,11:16.68035129161531):25.41308500675089,((((5:3.875932553123995,7:5.875932553123995):8.354465182969719,(4:13.880237985112942,2:15.880237985112942):2.3501597509807723):1.014667048417543,(1:24.629685195317254,9:12.629685195317254):3.615379589194003):2.0924913910034633,(17:12.20759626829663,15:10.20759626829663):10.12995990721809):28.75588012285148):46.65855617828947,(6:32.125071193023885,((8:36.51007344889376,(13:6.15700417146255,10:6.15700417146255):24.353069277431214):13.446389134111527,((3:27.93618745730774,12:7.936187457307739):15.117424113007246,16:15.053611570314985):6.902851012690306):3.1686086100185946):42.62692128363179);
tree STATE_3000 = [&R] (((14:20.483206149647202,11:21.483206149647202):22.93000050610265,((9:29.210365402953386,15:31.210365402953386):6.963878448862964,(((5:1.058670082529634,17:8.058670082529634):17.505417669414687,(1:29.293978752337733,(7:15.745058499414569,2:19.74505849941457):0.548920252923164):4.270108999606588):9.113992193128524,4:31.678079945072845):5.496163906743504):13.238962803933504):46.56279803141086,(6:66.7323674585687,((16:33.05907347236075,(12:34.39116008044314,3:54.39116008044314):6.667913391917608):14.430895055092819,(8:18.812830324317595,(13:12.023111758272048,10:12.023111758272048):0.789718566045547):56.677138203135975):12.242398931115133):10.243637228592007);
tree STATE_4000 = [&R] (((14:1.4232529520251838,11:2.4232529520251838):50.08209442255527,(((17:8.635455447984924,(5:0.04107298606299814,7:2.041072986062998):1.594382461921926):1.8904400680756765,((2:1.8627305818303324,15:0.8627305818303324):4.631707478329915,(9:1.156166746141075,4:2.156166746141075):2.338271314019172):3.0314574559003535):13.611383095498084,1:32.137278611558685):37.36806876302177):358.4106022580529,((((3:70.21675704721137,12:50.216757047211374):25.69095841819542,16:67.9077154654068):176.52655439813037,(8:33.491067730813526,(13:0.06462749292644787,10:0.06462749292644787):27.42644023788708):238.94320213272363):120.38145636713432,6:371.8157262306715):25.100223401961898);
tree STATE_5000 = [&R] ((13:2.666254155512604,((10:1.2936880844710643,8:7.293688084471064):0.3703955258231524,(5:0.002168417312294224,((15:3.035229598661715,7:0.035229598661715045):0.19225715947651523,(4:1.1191387107277873,(9:0.0728247412153209,((2:1.1756934708573112,17:2.1756934708573112):1.5742330689095958,3:1.749926539766907):0.32289820144841386):0.04631396951246636):1.108348047410443):1.774681659174064):2.6619151929819225):1.0021705452183873):227.00395413183298,(((6:4.4555158517863305,12:5.4555158517863305):4.1711212684822385,16:1.626637120268569):16.14642280672315,((14:0.4839440085462243,11:1.4839440085462243):5.449210005334351,1:23.933154013880575):31.839905913111146):189.89714836035387);
tree STATE_6000 = [&R] (6:15.136391733463448,(((13:7.410323714260258,(10:1.3348668082208306,8:7.334866808220831):6.0754569060394275):13.866399657737404,(((3:7.932330997136486,11:0.9323309971364857):0.5564983243726296,((7:0.43576630640882286,((9:0.16554245599578898,15:2.165542455995789):0.11405176338982237,4:1.2795942193856114):1.1561720870232115):1.979424175743116,((1:13.125246553707456,(2:3.210780781680455,17:4.210780781680455):0.9144657720270004):2.1761651865884577,5:0.30141174029591333):0.11377874185602543):3.0736388393571765):0.4220084645725919,14:0.9108377860817072):18.365885585915954):4.482436123116571,(12:8.32012369812879,16:0.32012369812878916):3.4390357969854435):4.377232238349215);
tree STATE_7000 = [&R] (6:17.65271520837951,(((13:12.612074134158078,(10:3.5755981409442903,8:9.57559814094429):9.036475993213788):12.611363326970618,(12:8.692284871803174,16:0.6922848718031744):2.5311525893255222):1.3687913448748077,(((3:9.150043873379396,11:2.1500438733793956):0.34971950625408255,14:1.4997633796334782):0.15520324399904695,(5:0.46991615662493125,(((7:0.5632707568059896,((4:1.6455158682383662,9:0.6455158682383662):0.6772628158015532,15:3.3227786840399194):0.2404920727660702):0.3660018536540246,(2:3.9589228739516322,17:4.958922873951632):0.970349736508382):0.371110505214558,1:14.300383115674572):1.169533040950359):4.185050467007594):22.93726218237098):6.060486402376007);
tree STATE_8000 = [&R] (6:18.919185710884868,(((3:21.408112871918796,12:1.4081128719187959):8.750013744808662,16:2.1581266167274578):4.049122885310588,((13:12.9574080076843,(10:4.329756013099772,8:10.329756013099772):8.627651994584529):11.39997558339681,((11:2.684372330230989,(5:1.6304936087947972,((((4:1.9165626486725014,15:2.9165626486725014):0.16555594914844463,(7:0.07393503841628934,9:1.0739350384162893):0.008183559404656648):0.7603541619063705,1:13.842472759727317):1.6046025811051567,(2:5.567661149721506,17:6.567661149721506):0.8794141911109676):1.183418267962324):3.0538787214361918):0.6144048612401782,14:2.298777191471167):20.058606399609943):3.849865910956936):5.711936208846822);
tree STATE_9000 = [&R] (6:24.725349638462184,(((11:2.661722003781282,(5:1.0847503934753462,(((((15:3.010203896437174,4:2.010203896437174):0.32711259459587794,9:1.337316491033052):0.07280070522472393,7:0.4101171962577759):1.3234416182346163,(2:3.6715986657467425,17:4.6715986657467425):2.0619601487456496):0.28890426713629225,1:15.022463081628684):1.0622873118466618):3.576971610305936):0.6370551876898851,14:2.298777191471167):35.29054824800323,((13:13.190131646726318,(10:3.134808494137623,8:9.134808494137623):10.055323152588695):16.4294277022645,((3:21.243794915007275,12:1.2437949150072747):8.38388598946884,16:1.6276809044761151):5.991878444514704):9.969766090483581):0.1360241989877835);
tree STATE_10000 = [&R] (6:24.96730757453785,(((11:1.6456140804102368,(5:1.3716719476098689,((2:5.170504147786595,17:6.170504147786595):1.6813080939193448,((((7:0.1519609628752825,9:1.1519609628752825):0.19171964313059497,4:2.3436806060058775):0.7026562733229316,15:4.046336879328809):0.4174301705220085,1:14.463767049850818):1.388045191855122):0.5198597059039294):2.273942132800368):1.357054362457049,14:2.002668442867286):29.7083330536181,((13:11.655336226312041,(10:3.5100441889805865,8:9.510044188980586):8.145292037331455):14.644140056694948,((3:23.004626069060237,12:3.0046260690602367):5.553573368011982,16:0.5581994370722185):3.7412768459347703):7.411525213478399):6.256306078052461);
End;
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1)
java -jar TreeCmp.jar -w 5 -d rf -i ALIGN1.nex -o ALIGN1.nex.w_5.out
2)
java -jar TreeCmp.jar -s -d tt ns mc rc -i ALIGN1.nex -o ALIGN1.nex_s.out
3)
java -jar TreeCmp.jar -m -d ms pd -i ALIGN1.nex -o ALIGN1.nex_m.out
\ No newline at end of file
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