P A U P *
Portable version 4.0b10 for Unix
Thu Jun 1 22:20:29 2006
NOTICE
This is a betatest version. Please report any crashes,
apparent calculation errors, or other anomalous results.
There are no restrictions on publication of results obtained
with this version, but you should check the WWW site
frequently for bug announcements and/or updated versions.
See the README file on the distribution media for details.

Processing of file "~/new_at_family_tcoffee/4_20/cds_nex_4_20/2356.fasta"
begins...
Warning: Use of alldigit taxon and/or character names does not conform to the
NEXUS standard and is strongly discouraged. Remember that names have
priority over numbers.
Data read in DNA format
Data matrix has 8 taxa, 441 characters
Valid characterstate symbols: ACGT
Missing data identified by '?'
Gaps identified by ''
"Equate" macros in effect:
R,r ==> {AG}
Y,y ==> {CT}
M,m ==> {AC}
K,k ==> {GT}
S,s ==> {CG}
W,w ==> {AT}
H,h ==> {ACT}
B,b ==> {CGT}
V,v ==> {ACG}
D,d ==> {AGT}
N,n ==> {ACGT}
Processing of file "~/new_at_family_tcoffee/4_20/cds_nex_4_20/2356.fasta"
completed.
Optimality criterion set to likelihood.
Heuristic search settings:
Optimality criterion = likelihood
Likelihood settings:
Number of substitution types = 2 (HKY85 variant)
Transition/transversion ratio = 0.9671 (kappa = 1.9683596)
Assumed nucleotide frequencies (set by user):
A=0.27230 C=0.21290 G=0.22250 T=0.29230
Amongsite rate variation:
Assumed proportion of invariable sites = none
Distribution of rates at variable sites = gamma (discrete
approximation)
Shape parameter (alpha) = 0.866
Number of rate categories = 4
Representation of average rate for each category = mean
These settings correspond to the HKY85+G model
Number of distinct data patterns under this model = 244
Molecular clock not enforced
Starting branch lengths obtained using RogersSwofford approximation
method
Trees with approximate likelihoods 5% or further from the target score
are rejected without additional iteration
Branchlength optimization = onedimensional NewtonRaphson with pass
limit=20, delta=1e06
ln L (unconstrained) = unavailable due to missingdata and/or
ambiguities
Starting tree(s) obtained via stepwise addition
Addition sequence: random
Number of replicates = 10
Starting seed = 76639959
Number of trees held at each step during stepwise addition = 1
Branchswapping algorithm: treebisectionreconnection (TBR)
Steepest descent option not in effect
Initial 'MaxTrees' setting = 100
Branches collapsed (creating polytomies) if branch length is less than or
equal to 1e08
'MulTrees' option in effect
Topological constraints not enforced
Trees are unrooted
Heuristic search completed
Total number of rearrangements tried = 306
Score of best tree(s) found = 2785.88995
Number of trees retained = 1
Time used = 17 sec (CPU time = 15.85 sec)
Treeisland profile:
First Last First Times
Island Size tree tree Score replicate hit

1 1 1 1 2785.88995 1 10
Tree description:
Unrooted tree(s) rooted using outgroup method
Optimality criterion = likelihood
Likelihood settings:
Number of substitution types = 2 (HKY85 variant)
Transition/transversion ratio = 0.9671 (kappa = 1.9683596)
Assumed nucleotide frequencies (set by user):
A=0.27230 C=0.21290 G=0.22250 T=0.29230
Amongsite rate variation:
Assumed proportion of invariable sites = none
Distribution of rates at variable sites = gamma (discrete
approximation)
Shape parameter (alpha) = 0.866
Number of rate categories = 4
Representation of average rate for each category = mean
These settings correspond to the HKY85+G model
Number of distinct data patterns under this model = 244
Molecular clock not enforced
Starting branch lengths obtained using RogersSwofford approximation
method
Branchlength optimization = onedimensional NewtonRaphson with pass
limit=20, delta=1e06
ln L (unconstrained) = unavailable due to missingdata and/or
ambiguities
Tree number 1 (rooted using default outgroup)
Branch lengths and linkages for tree #1 (unrooted)
Connected Branch Standard
Node to node length error

3735 (1) 14 0.01482 0.00695
9 14 0.01081 0.00638
71367 (2) 9 1.31779 0.17946
78678 (3) 9 0 0.00721
13 14 0.16780 0.03504
12 13 0.18267 0.03743
11 12 0.17377 0.03053
At2g41450.1 (4) 11 8.950e07 0.03167
10 11 6.14043 1.31769
At3g60950.1 (7) 10 0 undefined
At3g61030.1 (8) 10 0 undefined
At3g57200.1 (6) 12 0.10067 0.02513
At3g08550.1 (5) 13 0.24033 0.04029

Sum 8.34909
Ln likelihood = 2785.88995
/ 3735

+ 71367
9
+ 78678

14 / At2g41450.1
 
 /11 / At3g60950.1
  \10
 12 \ At3g61030.1
 
\13\ At3g57200.1

\ At3g08550.1
1 tree saved to file "~/new_at_family_tcoffee/4_20/trees_4_20/2356.ml.tre"