
                              EMBOSS: ednamlk
     _________________________________________________________________
   
                                Program ednamlk
                                       
Function

   Conversion of PHYLIP's dnamlk
   
Description

   EDNAMLK -- Embossified DNA Maximum Likelihood program with molecular
   clock
   
   Phylip dnamlk documentation.
   
Usage

   Here is a sample session with ednamlk.

% ednamlk test -options

Estimates phylogenies from nucleic acid sequence Maximum Likelihood with
molecular clock
Output file [ednamlk.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 than one category of substitution rates [N]: y
Number of categories of substitution rates [2]:
space seperated category values: 1.0 3.2
space seperated probabilliyy 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
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 [ednamlk.treefile]:

Nucleic acid sequence
   Maximum Likelihood method with molecular clock, 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)





                                                           +--Delta
  +--------------------------------------------------------4
  !                                                        +--Epsilon
--3
  !                                             +-------------Gamma
  +---------------------------------------------2
                                                !          +--Alpha
                                                +----------1
                                                           +--Beta


Ln Likelihood =   -72.40499

 Ancestor      Node      Node Time     Length
 --------      ----      ---- ----     ------
 root            3
   3             4         3.40036     3.40036
   4          Delta        3.55871     0.15834
   4          Epsilon      3.55871     0.15834
   3             2         2.75249     2.75249
   2          Gamma        3.55871     0.80621
   2             1         3.38652     0.63403
   1          Alpha        3.55871     0.17218
   1          Beta         3.55871     0.17218


Combination of categories that contributes the most to the likelihood:
             2222221111 112






% more ednamlk.treefile
((Delta:0.15834,Epsilon:0.15834):3.40036,(Gamma:0.80621,
(Alpha:0.17218,Beta:0.17218):0.63403):2.75249);

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)
  [-[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 than one category of substitution rates
   -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 ednamlk.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
   [-[no]trout]
   (Parameter 3) Create a tree file Yes/No Yes
   -treefile Tree file name Output file ednamlk.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 than one category of substitution rates 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
