P A U P *
Portable version 4.0b10 for Unix
Thu Jun 1 14:50:58 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_20/1303.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 14 taxa, 111 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_20/1303.fasta"
completed.
Optimality criterion set to likelihood.
Heuristic search settings:
Optimality criterion = likelihood
Likelihood settings:
Number of substitution types = 2
Transition/transversion ratio = 1.6328 (kappa = 3.2656)
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 = none
Distribution of rates at variable sites = gamma (discrete
approximation)
Shape parameter (alpha) = 0.7322
Number of rate categories = 4
Representation of average rate for each category = mean
These settings correspond to the K80(K2P)+G model
Number of distinct data patterns under this model = 57
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 = 900750440
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 7 14 7683 2 1 763.32283 763.32276
0:01:26 10  10908 1 0 763.32276 763.32276
Heuristic search completed
Total number of rearrangements tried = 10908
Score of best tree(s) found = 763.32276
Number of trees retained = 1
Time used = 00:01:26 (CPU time = 00:01:20.8)
Treeisland profile:
First Last First Times
Island Size tree tree Score replicate hit

1 1 1 1 763.32276 1 10
Tree description:
Unrooted tree(s) rooted using outgroup method
Optimality criterion = likelihood
Likelihood settings:
Number of substitution types = 2
Transition/transversion ratio = 1.6328 (kappa = 3.2656)
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 = none
Distribution of rates at variable sites = gamma (discrete
approximation)
Shape parameter (alpha) = 0.7322
Number of rate categories = 4
Representation of average rate for each category = mean
These settings correspond to the K80(K2P)+G model
Number of distinct data patterns under this model = 57
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

104701 (1) 25 0.24890 0.09063
24 25 0.11568 0.06819
19 24 0.12668 0.06467
18 19 0.09061 0.03220
16 18 0.00947 0.00972
15 16 0.04759 0.02213
27527 (2) 15 0 undefined
3504 (6) 15 0 undefined
99335 (12) 16 0.00947 0.00974
17 18 0.01919 0.01472
33343 (5) 17 0.08182 0.03082
77884 (9) 17 0.01886 0.01468
45010 (8) 18 0.03819 0.01961
29702 (3) 19 0 0.04258
23 24 0.23137 0.07871
32271 (4) 23 0 0.01883
22 23 0.00999 0.01026
41477 (7) 22 0.06067 0.02584
21 22 0.00842 0.00946
80126 (10) 21 0 undefined
20 21 0.04881 0.02256
9625 (11) 20 0 0.03127
At2g20820.2 (14) 20 2.13660 0.62891
At2g20820.1 (13) 25 0.28618 0.09808

Sum 3.58850
Ln likelihood = 763.32276
/ 104701

 / 27527
 15
 \ 3504
 16
 + 99335
 
 + 33343
 /17
  + 77884
  
 /19 \ 45010
25  
  \ 29702
+24
  / 32271
  
 \23 41477
 
 22 80126
 
 21 / 9625
 \20
 \ At2g20820.2

\ At2g20820.1
1 tree saved to file "~/new_at_family_tcoffee/4_20/trees_4_20/1303.ml.tre"