#NEXUS
 

[
**partial output for r8s analysis of Pinusaug07PINS123maxnov07age.out]**

Executing blformat command...
Branch lengths assumed to be in units of numbers of substitutions per site
Number of sites in sequences set to 2708
All branch lengths multipled by the 2708 sites in the sequence
Branch lengths rounded to nearest integer
(This may not be a good idea when using CALIBRATE on ultrametric user supplied input trees. Use ROUND=NO then)
Pruning taxon Sciadopit
Pruning taxon Cryptomer
Pruning taxon Amentotax
Pruning taxon Podocarpu
Pruning taxon Ginbiloba
2 zero-length branches collapsed
Defining clade name: ABKE
Defining clade name: PLTS
Defining clade name: ABCE
Defining clade name: ABPL
Defining clade name: PSLA
Defining clade name: PINS
Defining clade name: PINC
Defining clade name: PARR
Defining clade name: ARPI
Fixing age of PINS at 123.000000
(The age of this node will no longer be estimated.)
(This command overides any previous age constraints for this node.)
(The total number of fixed ages is now 1)
Setting maximum age constraint for taxon ARPI to 308.500000
Setting minimum age constraint for taxon PSLA to 45.500000
Setting minimum age constraint for taxon ABKE to 45.500000
Setting minimum age constraint for taxon PARR to 27.200000

----------------------------------------

LINEAGE RATE/TIME ANALYSIS FOR TREE PAUP_1

Method = Penalized Likelihood
Smoothing factor = 100.000000
Penalty function = Ancestor-Descendant
Scale for rate penalty = ADDITIVE
Minimum allowed rate = 0.050000 of initial average rate estimate
Minimum allowed duration on 0-length terminal branches = 0.001000 of root's age
Optimization via Truncated-Newton (TN) method with bound constraints

----------------------------------------
Substitution Model
Rates are equal across sites
Global/Local Search Parameters
Number of searches from random starts = 5
Number of restarts after each search = 3
Local perturbation on restarts = 0.05
Local fractional tolerance after restarts = 0.01
Optimization parameters set automatically by TN routine
Length of tree input = 1205
Number of taxa = 44
Number of sites in sequences = 2708

]

begin trees;

tree PAUP_1 = ((((((((((johannis8:7.974928,cembroide:7.974928):2.587022,pinceana8:10.561950,rzedowski:10.561950):2.200474,monophy23:12.762423):14.437577,(nelsonii3:23.212318,((aristata3:9.115030,longae309:9.115030):1.641264,balfouria:10.756294):12.456024):3.987682)PARR:10.196848,(((bungeana2:5.850477,gerardi12:5.850477):1.686717,squamata0:7.537194):13.557293,krempfiiL:21.094488,(peuce0427:13.398977,(strobus50:9.451075,(monticola:4.752381,cembra106:4.752381):4.698695):3.947902):7.695510):16.302360):37.984610,(((contorta4:5.423290,BANKListo:5.423290):12.685377,((montezuma:2.856962,devoniana:2.856962):7.912265,(pungeGret:5.663030,(leiophyll:4.107609,radiata37:4.107609):1.555421,palustris:5.663030):5.106197):7.339440):9.123704,((heldListo:11.346185,(roxburg06:9.418478,pineaKew3:9.418478,halepGret:9.418478):1.927707):3.429398,(resinosa:6.826548,((nigraGret:4.633214,sylvestri:4.633214):0.729653,thunbergi:5.362867):1.463681):7.949036):12.456787):48.149087)PINC:54.618542,(Pisitchen:118.377647,Cathaya22:118.377647):11.622353)PINS:6.967009,(Lgmelinii:82.083904,Pmenziesi:82.083904)PSLA:54.883104):9.276842,(((Pseudamab:84.855025,(Tcanadens:43.656993,Notholong:43.656993):41.198032)PLTS:9.914486,(Abhidalge:65.611413,KetdavidD:65.611413)ABKE:29.158099):26.332310,Cedeodara:121.101821):25.142030):161.756149,Araraucan:308.000000)ARPI;
end;