| ## EMBOSS: econtml

# Program econtml

## Function

Conversion of PHYLIP's contml

## Description

ECONTML - Gene Frequencies and Continuous Characters Maximum Likelihood method

Phylip contml documentation.

## Usage

Here is a sample session with econtml using the data:-

       5    10
    2 2 2 2 2 2 2 2 2 2
    European   0.2868 0.5684 0.4422 0.4286 0.3828 0.7285 0.6386 0.0205 0.8055 0.5043
    African    0.1356 0.4840 0.0602 0.0397 0.5977 0.9675 0.9511 0.0600 0.7582 0.6207
    Chinese    0.1628 0.5958 0.7298 1.0000 0.3811 0.7986 0.7782 0.0726 0.7482 0.7334
    American   0.0144 0.6990 0.3280 0.7421 0.6606 0.8603 0.7924 0.0000 0.8086 0.8636
    Australian 0.1211 0.2274 0.5821 1.0000 0.2018 0.9000 0.9837 0.0396 0.9097 0.2976

    % econtml test

    Continuous character Maximum Likelihood method
    Output file [econtml.outfile]: stdout
    Global rearrangements [N]:
    Randomize input order of species [N]:
    Input file has all alleles at each locus [N]:
    Create a tree file [Y]:
    Output treefile name [econtml.treefile]:

       5 Populations,   10 Loci

      +----------------------------------African
      !
      !              +--------American
    --1--------------2
      !              !                    +-----------------------Australian
      !              +--------------------3
      !                                   +Chinese
      !
      +--European

    remember: this is an unrooted tree!

    Ln Likelihood =    33.29060

    examined   15 trees

    Between     And             Length      Approx. Confidence Limits
    -------     ---             ------      ------- ---------- ------
      1       African           0.08464   (     0.02351,     0.17917)
      1          2              0.03569   (    -0.00262,     0.09493)
      2       American          0.02094   (    -0.00904,     0.06731)
      2          3              0.05098   (     0.00555,     0.12124)
      3       Australian        0.05959   (     0.01775,     0.12430)
      3       Chinese           0.00221   (    -0.02034,     0.03710)
      1       European          0.00624   (    -0.01948,     0.04601)

    % more econtml.treefile
    (African:0.08464,(American:0.02094,(Australian:0.05959,Chinese:0.00221):0.05098):0.03569,
    European:0.00624);

## Command line arguments

       Mandatory qualifiers (* if not always prompted):
      [-infile]            infile     input file
      [-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)
    *  -all                bool       Input file has all alleles at each locus
    *  -outgnum            integer    number of the outgroup
    *  -datasets           integer    How many data sets
      [-[no]trout]         bool       Create a tree file
    *  -treefile           outfile    Tree file name

       Optional qualifiers:
       -[no]besttree       bool       Search for best tree
       -continuous         bool       continuous characters (else Gene
                                      frequencies)
       -og                 bool       Outgroup root
       -multsets           bool       Analyze multiple data sets
       -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
--- | --- | ---
[-infile] (Parameter 1) | input file | Input file | Required
[-outfile] (Parameter 2) | Output file name | Output file | econtml.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
-all | Input file has all alleles at each locus | Yes/No | No
-outgnum | number of the outgroup | Integer 1 or more | 1
-datasets | How many data sets | Integer 1 or more | 1
[-[no]trout] (Parameter 3) | Create a tree file | Yes/No | Yes
-treefile | Tree file name | Output file | econtml.treefile
Optional qualifiers | Allowed values | Default
-[no]besttree | Search for best tree | Yes/No | Yes
-continuous | continuous characters (else Gene frequencies) | Yes/No | No
-og | Outgroup root | Yes/No | No
-multsets | Analyze multiple data sets | 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)

## Input file format

## Output file format

## Data files

## Notes

## 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