P A U P *
Portable version 4.0b10 for Unix
Sat Jun 3 06:10:51 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_20/57105.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 17 taxa, 225 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_20/57105.fasta"
completed.
Optimality criterion set to likelihood.
Heuristic search settings:
Optimality criterion = likelihood
Likelihood settings:
Number of substitution types = 2
Transition/transversion ratio = 1.013 (kappa = 2.026)
Assumed nucleotide frequencies (set by user):
A=0.25000 C=0.25000 G=0.25000 T=0.25000
Amongsite rate variation:
Assumed proportion of invariable sites = 0.0575
Distribution of rates at variable sites = gamma (discrete
approximation)
Shape parameter (alpha) = 2.8012
Number of rate categories = 4
Representation of average rate for each category = mean
These settings correspond to the K80(K2P)+G+I model
Number of distinct data patterns under this model = 207
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) = 1195.39538
Starting tree(s) obtained via stepwise addition
Addition sequence: random
Number of replicates = 10
Starting seed = 756636577
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
Elapsed Random Taxa Rearr.  No. of trees   Best trees 
time rep added tried saved lefttoswap this rep overall

0:01:00 1 17 1458 1 1 3681.7065 3681.7065
Note: Approximation limit dynamically readjusted to 14.044882
0:02:02 3 16 2788    3681.7065
0:03:02 5 12 4003    3681.7065
0:04:02 7  4733 2 1 3682.7948 3681.7065
0:05:02 8  6020 2 1 3682.1937 3681.7065
0:06:02 9  7403 2 1 3685.3484 3681.7065
0:06:26 10  7745 1 0 3681.7065 3681.7065
Heuristic search completed
Total number of rearrangements tried = 7745
Score of best tree(s) found = 3681.70646
Number of trees retained = 1
Time used = 00:06:26 (CPU time = 00:06:25.8)
Treeisland profile:
First Last First Times
Island Size tree tree Score replicate hit

1 1 1 1 3681.70646 1 10
Tree description:
Unrooted tree(s) rooted using outgroup method
Optimality criterion = likelihood
Likelihood settings:
Number of substitution types = 2
Transition/transversion ratio = 1.013 (kappa = 2.026)
Assumed nucleotide frequencies (set by user):
A=0.25000 C=0.25000 G=0.25000 T=0.25000
Amongsite rate variation:
Assumed proportion of invariable sites = 0.0575
Distribution of rates at variable sites = gamma (discrete
approximation)
Shape parameter (alpha) = 2.8012
Number of rate categories = 4
Representation of average rate for each category = mean
These settings correspond to the K80(K2P)+G+I model
Number of distinct data patterns under this model = 207
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) = 1195.39538
Tree number 1 (rooted using default outgroup)
Branch lengths and linkages for tree #1 (unrooted)
Connected Branch Standard
Node to node length error

104193 (1) 32 0.16253 0.04040
24 32 0.01600 0.03871
18 24 0.20179 0.04538
79083 (2) 18 0.02167 0.01241
9734 (3) 18 0.02431 0.01280
23 24 0.37260 0.11896
At1g03390.1 (4) 23 0.61236 0.13603
22 23 0.27322 0.13276
21 22 0.34854 0.14457
19 21 0.44379 0.12718
At2g23510.1 (7) 19 0.35059 0.08611
At2g25150.1 (8) 19 0.37805 0.08850
20 21 0.21148 0.09919
At3g47170.1 (10) 20 0.25904 0.05963
At5g07080.1 (14) 20 0.19004 0.05610
At3g62160.1 (12) 22 0.81215 0.18289
31 32 0.10005 0.03836
29 31 0.17621 0.05241
27 29 0.04591 0.06245
25 27 0.34630 0.11799
At1g27620.1 (5) 25 0.86208 0.17233
At2g40230.1 (9) 25 0.47365 0.11960
26 27 0.24200 0.09700
At1g65450.1 (6) 26 0.49096 0.11423
At4g31910.1 (13) 26 0.90337 0.17560
28 29 0.10627 0.04359
At3g48720.1 (11) 28 0.10570 0.03050
At5g63560.1 (17) 28 0.11368 0.03123
30 31 0.19236 0.04539
At5g41040.1 (15) 30 0 undefined
At5g41040.2 (16) 30 0 undefined

Sum 8.83670
Ln likelihood = 3681.70646
/ 104193

 / 79083
/18
 \ 9734

 / At1g03390.1
24 
  / At2g23510.1
  /19
\23  \ At2g25150.1
  /21
    / At3g47170.1
   \20
32 \22 \ At5g07080.1
 
 \ At3g62160.1

 / At1g27620.1
 /25
  \ At2g40230.1
 /27
   / At1g65450.1
  \26
 /29 \ At4g31910.1
  
   / At3g48720.1
  \28
\31 \ At5g63560.1

 / At5g41040.1
\30
\ At5g41040.2
1 tree saved to file "~/new_at_family_tcoffee/4_20/trees_4_20/57105.ml.tre"