
                               EMBOSS: ednaml
     _________________________________________________________________
   
                                Program ednaml
                                       
Function

   Conversion of PHYLIP's dnaml
   
Description

   EDNAML -- Embossified DNA Maximum Likelihood program
   
   Phylip dnaml documentation.
   
Usage

   Here is a sample session with ednaml using the test data:-
   5   13
Alpha     AACGTGGCCAAAT
Beta      AAGGTCGCCAAAC
Gamma     CATTTCGTCACAA
Delta     GGTATTTCGGCCT
Epsilon   GGGATCTCGGCCC


run with two categories with rates 1.0 and 3.2, and with
probabilities 0.4 and 0.6 for these rates, and with patch length
parameter = 1.5

% ednaml test -options

Estimates phylogenies from nucleic acid sequence Maximum Likelihood
Output file [ednaml.outfile]: stdout
Search for best tree [Y]:
Global rearrangements [N]:
Randomize input order of species [N]:
Transition/transversion ratio [2.0]:
Use empirical base frequencies [Y]:
More then one category of substitution rates [N]: y
Number of categories of substitution rates [2]:
space seperated categorie values: 1.0 3.2
space seperated probabillity values: 0.4 0.6
Use Defualt Mean block length of sites [N]:
Mean block length of sites having the same rate (greater than 1) [1.0]: 1.5
Outgroup root [N]:
Print out the data at start of run [N]:
Print indications of progress of run [N]:
Draw tree [Y]:
Create a tree file [Y]:
Output treefile name [ednaml.treefile]:


Nucleic acid sequence Maximum Likelihood method, version 3.573c



Site category   Rate of change    Probability

           1        1.000            0.400
           2        3.200            0.600


Expected length of a patch of sites having the same rate =    1.500

Empirical Base Frequencies:

   A       0.24615
   C       0.29231
   G       0.24615
  T(U)     0.21538


Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.523077)


                                                       +Epsilon
     +-------------------------------------------------3
  +--2                                                 +----Delta
  !  !
  !  +Beta
  !
--1---------------------Gamma
  !
  +---Alpha


remember: this is an unrooted tree!

Ln Likelihood =   -72.22209

Examined   15 trees

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

   1             2              0.06470     (     zero,     0.47007)
   2             3              3.33631     (     zero,    12.06173) **
   3          Epsilon           0.00003     (     zero,     0.42144)
   3          Delta             0.31956     (     zero,     0.73912) **
   2          Beta              0.00003     (     zero,     0.41860)
   1          Gamma             1.47621     (     zero,     3.63348) **
   1          Alpha             0.28041     (     zero,     0.73601) *

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01

Combination of categories that contributes the most to the likelihood:

             2222111111 222




% more ednaml.treefile
(((Epsilon:0.00012,Delta:0.31956):3.33631,Beta:0.00012):0.06470,Gamma:1.47621,A
lpha:0.28041);



Command line arguments

   Mandatory qualifiers (* if not always prompted):
  [-msf]               seqset     File containing a sequence allignment
  [-outfile]           outfile    Output file name
*  -lengths            bool       Use lengths from user trees
*  -global             bool       Global rearrangements
*  -random             bool       Randomize input order of species
*  -randseed           integer    Random number seed (must be odd)
*  -randtimes          integer    How many times to randomise
*  -freqa              float      Frequency for A
*  -freqc              float      Frequency for C
*  -freqg              float      Frequency for G
*  -freqt              float      Frequency for T/U
*  -catnum             integer    Number of categories of substitution rates
*  -catvals            string     space seperated category values
*  -catprob            string     space seperated probabillity values
*  -autog              bool       Use Defualt Mean block length of sites
*  -lambda             float      Mean block length of sites having the same
                                  rate (greater than 1)
*  -outgnum            integer    number of the outgroup
  [-[no]trout]         bool       Create a tree file
*  -treefile           outfile    Tree file name

   Optional qualifiers:
   -[no]besttree       bool       Search for best tree
   -ttratio            float      Transition/transversion ratio
   -[no]basefrequency  bool       Use empirical base frequencies
   -categories         bool       More then one category of substitution rates
   -og                 bool       Outgroup root
   -printdata          bool       Print out the data at start of run
   -progress           bool       Print indications of progress of run
   -[no]drawtree       bool       Draw tree

   Advanced qualifiers: (none)
   
   Mandatory qualifiers Allowed values Default
   [-msf]
   (Parameter 1) File containing a sequence allignment Readable sequences
   Required
   [-outfile]
   (Parameter 2) Output file name Output file ednaml.outfile
   -lengths Use lengths from user trees Yes/No No
   -global Global rearrangements Yes/No No
   -random Randomize input order of species Yes/No No
   -randseed Random number seed (must be odd) Any integer value 3
   -randtimes How many times to randomise Any integer value 3
   -freqa Frequency for A Number from 0.000 to 1.000 0.25
   -freqc Frequency for C Number from 0.000 to 1.000 0.25
   -freqg Frequency for G Number from 0.000 to 1.000 0.25
   -freqt Frequency for T/U Number from 0.000 to 1.000 0.25
   -catnum Number of categories of substitution rates Integer from 2 to 9
   2
   -catvals space seperated category values Any string is accepted An
   empty string is accepted
   -catprob space seperated probabillity values Any string is accepted An
   empty string is accepted
   -autog Use Defualt Mean block length of sites Yes/No No
   -lambda Mean block length of sites having the same rate (greater than
   1) Number 1.000 or more 1.0
   -outgnum number of the outgroup Integer 1 or more 1
   [-[no]trout]
   (Parameter 3) Create a tree file Yes/No Yes
   -treefile Tree file name Output file ednaml.treefile
   Optional qualifiers Allowed values Default
   -[no]besttree Search for best tree Yes/No Yes
   -ttratio Transition/transversion ratio Any integer value 2.0
   -[no]basefrequency Use empirical base frequencies Yes/No Yes
   -categories More then one category of substitution rates Yes/No No
   -og Outgroup root Yes/No No
   -printdata Print out the data at start of run Yes/No No
   -progress Print indications of progress of run Yes/No No
   -[no]drawtree Draw tree Yes/No Yes
   Advanced qualifiers Allowed values Default
   (none)
   
Data files

Notes

   Multiple sequences sets not implemented yet!.
   
References

Warnings

Diagnostics

Exit status

Known bugs

See also

Author(s)

   (c) Copyright 1986-1993 by Joseph Felsenstein and by the University of
   Washington. Written by Joseph Felsenstein. Permission is granted to
   copy this document provided that no fee is charged for it and that
   this copyright notice is not removed.
   
   This application was modified for inclusion in EMBOSS by Ian Longden
   (il@sanger.ac.uk) Informatics Division, The Sanger Centre, Wellcome
   Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
   
Priority

Target users

Comments
