	From: 	  phyml@lirmm.fr
	Subject: 	phyml online results
	Date: 	30 August 2006 19:13:21 BDT
	To: 	  xxx@yyy.zzz
	Reply-To: 	  phyml@lirmm.fr


Your inferred tree is in attachment in Newick format
Manipulate this tree by clicking on the link below (active for 10 days)
http://atgc.lirmm.fr/phyml/scripts/ATVtree.php?tree=exec/xD242H192920_0/data.phy_phyml_tree.txt&email=xxx@yyy.zzz


- PHYML v2.4.4 -

. Sequence file : [/local/www/html/phyml/exec/xD242H192920_0/data.phy]

. Model of nucleotides substitution : GTR

. Initial tree : [BIONJ]

. Number of taxa : 10


. Likelihood : loglk = -3399.00103

. Discrete gamma model : Yes
  - Number of categories : 4
  - Gamma shape parameter : 0.321

. Nucleotides frequencies :

  - f(A)= 0.10380
  - f(C)= 0.21020
  - f(G)= 0.26140
  - f(T)= 0.42460

. GTR relative rate parameters : 

A <-> C    2.17589
A <-> G    3.83520
A <-> T    3.96104
C <-> G    6.51481
C <-> T    5.63071
G <-> T   1.0 (fixed)


. Instantaneous rate matrix : 

[A---------C---------G---------T------]
-1.21059   0.17624   0.38629   0.64806  
 0.08703  -1.66445   0.65619   0.92123  
 0.15339   0.52767  -0.84467   0.16361  
 0.15843   0.45606   0.10072  -0.71521  

eg., the instantaneous rate of change from 'C' to 'A' is  0.10380 x  2.17589 =  0.08703

. Time used 0h43m58s
. -> 2638 seconds

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%






Sequence filename : 				 /local/www/html/phyml/exec/xD242H192920_0/data.phy
Data type :             			 dna
Sequence format : 				 interleaved
Number of data sets : 				 1
Nb of bootstrapped data sets : 			 200
Model name : 					 GTR
Proportion of invariable sites :		 0.000000
Number of subst. rate categs : 			 4
Gamma distribution parameter : 			 estimated
Starting tree : 				 BIONJ
Optimise tree topology : 			 yes
Optimise branch lengths and rate parameters : 	 yes

. Compressing sequences...

. Computing pairwise distances...

. Building BIONJ tree...

. Log(lk) :               * ->    -3573.980664 
. Log(lk) :    -3573.980664 ->    -3544.005056   0 swap  done
. Log(lk) :    -3544.005056 ->    -3542.823250   0 swap  done
. Log(lk) :    -3542.823250 ->    -3542.685180   0 swap  done

. Optimisation of the GTR parameters...

. Optimisation of the gamma shape parameter...

. Log(lk) :    -3421.384960 ->    -3412.926914   1 swap  done
. Log(lk) :    -3412.926914 ->    -3409.888028   0 swap  done
. Log(lk) :    -3409.888028 ->    -3408.507444   1 swap  done
. Log(lk) :    -3408.507444 ->    -3407.740608   0 swap  done

. Optimisation of the GTR parameters...

. Optimisation of the gamma shape parameter...

. Log(lk) :    -3402.874519 ->    -3401.492227   1 swap  done
. Log(lk) :    -3401.492227 ->    -3400.756384   0 swap  done
. Log(lk) :    -3400.756384 ->    -3400.433874   0 swap  done
. Log(lk) :    -3400.433874 ->    -3400.266339   0 swap  done

. Optimisation of the GTR parameters...

. Optimisation of the gamma shape parameter...

. Log(lk) :    -3399.842107 ->    -3399.585236   0 swap  done
. Log(lk) :    -3399.585236 ->    -3399.449637   0 swap  done
. Log(lk) :    -3399.449637 ->    -3399.374399   0 swap  done

. Last optimization step...

. Log(lk) :               * ->    -3399.306991 

. Optimisation of the GTR parameters...

. Optimisation of the gamma shape parameter...

. Log(lk) :    -3399.306991 ->    -3399.133039 

. Optimisation of the GTR parameters...

. Optimisation of the gamma shape parameter...

. Log(lk) :    -3399.133039 ->    -3399.065623 

. Optimisation of the GTR parameters...

. Optimisation of the gamma shape parameter...

. Log(lk) :    -3399.065623 ->    -3399.032256 

. Optimisation of the GTR parameters...

. Optimisation of the gamma shape parameter...

. Log(lk) :    -3399.032256 ->    -3399.016012 

. Optimisation of the GTR parameters...

. Optimisation of the gamma shape parameter...

. Log(lk) :    -3399.016012 ->    -3399.008201 

. Optimisation of the GTR parameters...

. Optimisation of the gamma shape parameter...

. Log(lk) :    -3399.008201 ->    -3399.004492 

. Optimisation of the GTR parameters...

. Optimisation of the gamma shape parameter...

. Log(lk) :    -3399.004492 ->    -3399.002726 

. Optimisation of the GTR parameters...

. Optimisation of the gamma shape parameter...

. Log(lk) :    -3399.002726 ->    -3399.001890 

. Optimisation of the GTR parameters...

. Optimisation of the gamma shape parameter...

. Log(lk) :    -3399.001890 ->    -3399.001458 

. Optimisation of the GTR parameters...

. Optimisation of the gamma shape parameter...

. Log(lk) :    -3399.001458 ->    -3399.001258 

. Optimisation of the GTR parameters...

. Optimisation of the gamma shape parameter...

. Log(lk) :    -3399.001258 ->    -3399.001142 

. Optimisation of the GTR parameters...

. Optimisation of the gamma shape parameter...

. Log(lk) :    -3399.001142 ->    -3399.001089 

. Optimisation of the GTR parameters...

. Optimisation of the gamma shape parameter...

. Log(lk) :    -3399.001089 ->    -3399.001058 

. Optimisation of the GTR parameters...

. Optimisation of the gamma shape parameter...

. Log(lk) :    -3399.001058 ->    -3399.001044 

. Optimisation of the GTR parameters...

. Optimisation of the gamma shape parameter...

. Log(lk) :    -3399.001044 ->    -3399.001035 

. Optimisation of the GTR parameters...

. Optimisation of the gamma shape parameter...

. Log(lk) :    -3399.001035 ->    -3399.001031 

. Optimisation of the GTR parameters...

. Optimisation of the gamma shape parameter...

. Log(lk) :    -3399.001031 ->    -3399.001029 

. Optimisation of the GTR parameters...

. Optimisation of the gamma shape parameter...

. Log(lk) :    -3399.001029 ->    -3399.001027 

. Optimisation of the GTR parameters...

. Optimisation of the gamma shape parameter...

. Log(lk) :    -3399.001027 ->    -3399.001026 

. Optimisation of the GTR parameters...

. Optimisation of the gamma shape parameter...


. Non parametric bootstrap analysis 

  [..........] 10/200
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  [..........] 200/200



. Time used 0h43m58s

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%



- PHYML v2.4.4 -

. Sequence file : [/local/www/html/phyml/exec/xD242H192920_0/data.phy]

. Model of nucleotides substitution : GTR

. Initial tree : [BIONJ]

. Number of taxa : 10


. Likelihood : loglk = -3399.00103

. Discrete gamma model : Yes
  - Number of categories : 4
  - Gamma shape parameter : 0.321

. Nucleotides frequencies :

  - f(A)= 0.10380
  - f(C)= 0.21020
  - f(G)= 0.26140
  - f(T)= 0.42460

. GTR relative rate parameters : 

A <-> C    2.17589
A <-> G    3.83520
A <-> T    3.96104
C <-> G    6.51481
C <-> T    5.63071
G <-> T   1.0 (fixed)


. Instantaneous rate matrix : 

[A---------C---------G---------T------]
-1.21059   0.17624   0.38629   0.64806  
 0.08703  -1.66445   0.65619   0.92123  
 0.15339   0.52767  -0.84467   0.16361  
 0.15843   0.45606   0.10072  -0.71521  

eg., the instantaneous rate of change from 'C' to 'A' is  0.10380 x  2.17589 =  0.08703

. Time used 0h43m58s
. -> 2638 seconds

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

(((((((H:0.368014,(I:0.040232,D:0.210916)169:0.048124)116:0.044626,E:0.126443)191:0.100586,G:0.386759)104:0.015541,C:0.291688)197:0.191161,J:0.195844)194:0.151995,B:0.798487)111:0.000968,F:0.504085,A:0.263339);

