EMBOSS: erestml

| ## EMBOSS: erestml

# Program erestml

## Function

Conversion of PHYLIP's restml

## Description

ERESTML -- Embossified restriction sites Maximum Likelihood program

Phylip restml documentation.

## Usage

Here is a sample session with erestml uisng the data :-

       5   13   2
    Alpha     ++-+-++--+++-
    Beta      ++++--+--+++-
    Gamma     -+--+-++-+-++
    Delta     ++-+----++---
    Epsilon   ++++----++---

    % erestml test

    Restriction site Maximum Likelihood method
    Output file [erestml.outfile]: stdout
    Randomize input order of species [N]:
    Create a tree file [Y]:
    Output treefile name [erestml.treefile]:

    Restriction site Maximum Likelihood method, version 3.573c

      Recognition sequences all 6 bases long

    Sites absent from all species are assumed to have been omitted

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

    remember: this is an unrooted tree!

    Ln Likelihood =   -40.35857

    Examined   15 trees

     Between        And            Length      Approx. Confidence Limits
     -------        ---            ------      ------- ---------- ------
       2             3            0.05855     (  0.05681,     0.06030) **
       3          Epsilon         0.00005     (  0.00000,     0.00010)
       3          Delta           0.01458     (  0.01374,     0.01543) **
       2             1            0.00002     (     zero,     0.00006)
       1          Gamma           0.11430     (  0.11177,     0.11683) **
       1          Beta            0.00008     (  0.00002,     0.00014)
       2          Alpha           0.02468     (  0.02357,     0.02578) **

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

    % more erestml.treefile
    ((Epsilon:0.00005,Delta:0.01458):0.05855,(Gamma:0.11430,
    Beta:0.00008):0.00002,Alpha:0.02468);

## Command line arguments

       Mandatory qualifiers (* if not always prompted):
      [-datafile]          infile     Input file
      [-outfile]           outfile    Output file name
    *  -random             bool       Randomize input order of species
    *  -randseed           integer    Random number seed (must be odd)
    *  -randtimes          integer    How many times to randomise
    *  -outgnum            integer    number of the outgroup
    *  -datasets           integer    number of sets
      [-[no]trout]         bool       Create a tree file
    *  -treefile           outfile    Tree file name

       Optional qualifiers (* if not always prompted):
       -[no]besttree       bool       Search for best tree
       -[no]allsites       bool       Are all sites detected
    *  -lengths            bool       Use lengths from user trees
       -sitelen            integer    Site length
       -extrap             float      Extrapolation factor
    *  -global             bool       Global rearrangements
       -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
--- | --- | ---
[-datafile] (Parameter 1) | Input file | Input file | Required
[-outfile] (Parameter 2) | Output file name | Output file | erestml.outfile
-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
-outgnum | number of the outgroup | Integer 1 or more | 1
-datasets | number of sets | Integer 2 or more | 2
[-[no]trout] (Parameter 3) | Create a tree file | Yes/No | Yes
-treefile | Tree file name | Output file | erestml.treefile
Optional qualifiers | Allowed values | Default
-[no]besttree | Search for best tree | Yes/No | Yes
-[no]allsites | Are all sites detected | Yes/No | Yes
-lengths | Use lengths from user trees | Yes/No | No
-sitelen | Site length | Integer from 1 to 8 | 6
-extrap | Extrapolation factor | Number 0.001 or more | 100.0
-global | Global rearrangements | 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