| ## 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,Alpha: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