EMBOSS: econsense

| ## EMBOSS: econsense

# Program econsense

## Function

Conversion of PHYLIP's consense

## Description

ECONSENSE -- Embossified consensus tree program

Phylip consense documentation.

## Usage

Here is a sample session with econsense using the test data :-

    (A,(B,(H,(D,(J,(((G,E),(F,I)),C))))));
    (A,(B,(D,((J,H),(((G,E),(F,I)),C)))));
    (A,(B,(D,(H,(J,(((G,E),(F,I)),C))))));
    (A,(B,(E,(G,((F,I),((J,(H,D)),C))))));
    (A,(B,(E,(G,((F,I),(((J,H),D),C))))));
    (A,(B,(E,((F,I),(G,((J,(H,D)),C))))));
    (A,(B,(E,((F,I),(G,(((J,H),D),C))))));
    (A,(B,(E,((G,(F,I)),((J,(H,D)),C)))));
    (A,(B,(E,((G,(F,I)),(((J,H),D),C)))));

    % econsense test
    Majority-rule and strict consensus tree
    Output file [econsense.outfile]: stdout
    Create a tree file [Y]:
    tree file [econsense.treefile]:

    Majority-rule and strict consensus tree program, version 3.573c

    Species in order:

      A
      B
      H
      D
      J
      G
      E
      F
      I
      C

    Sets included in the consensus tree

    Set (species in order)     How many times out of   9.00

    .......**.                   9.00
    ..********                   9.00
    ..***....*                   6.00
    ..****.***                   6.00
    ..***.....                   6.00
    ..*.*.....                   4.00
    ..***..***                   2.00

    Sets NOT included in consensus tree:

    Set (species in order)     How many times out of   9.00

    .....**...                   3.00
    .....****.                   3.00
    ..**......                   3.00
    .....*****                   3.00
    ..*.******                   2.00
    .....*.**.                   2.00
    ..****...*                   2.00
    ....******                   2.00
    ...*******                   1.00

    CONSENSUS TREE:
    the numbers at the forks indicate the number
    of times the group consisting of the species
    which are to the right of that fork occurred
    among the trees, out of   9.00 trees

      +---------------------------------------A
      !
      !         +-----------------------------E
      !         !
      !         !                        +----I
      !         !         +------------9.0
      !         !         !              +----F
      !    +--9.0         !
      !    !    !    +--2.0         +---------D
      !    !    !    !    !    +--6.0
      !    !    !    !    !    !    !    +----J
      !    !    !    !    +--6.0    +--4.0
      +--9.0    +--6.0         !         +----H
           !         !         !
           !         !         +--------------C
           !         !
           !         +------------------------G
           !
           +----------------------------------B

      remember: this is an unrooted tree!

    % more econsense.treefile
    (A:9.0,((E:9.0,(((I:9.0,F:9.0):9.0,((D:9.0,(J:9.0,H:9.0):4.0):6.0,C:9.0):6.0):2.0,G:9.0):6.0):9.0,
    B:9.0):9.0);

## Command line arguments

       Mandatory qualifiers (* if not always prompted):
      [-infile]            infile     file to read in (New Hampshire standard
                                      form)
      [-outfile]           outfile    Output file name
      [-[no]trout]         bool       Create a tree file
      [-treefile]          outfile    tree file name
    *  -og                 bool       Outgroup root
    *  -outgnum            integer    number of the outgroup

       Optional qualifiers:
       -[no]drawtree       bool       Draw tree
       -root               bool       Trees to be treated as Rooted
       -progress           bool       Print indications of progress of run
       -[no]printsets      bool       Print out the sets of species

       Advanced qualifiers: (none)

Mandatory qualifiers | Allowed values | Default
--- | --- | ---
[-infile] (Parameter 1) | file to read in (New Hampshire standard form) | Input file | Required
[-outfile] (Parameter 2) | Output file name | Output file | econsense.outfile
[-[no]trout] (Parameter 3) | Create a tree file | Yes/No | Yes
[-treefile] (Parameter 4) | tree file name | Output file | econsense.treefile
-og | Outgroup root | Yes/No | No
-outgnum | number of the outgroup | Integer 1 or more | 1
Optional qualifiers | Allowed values | Default
-[no]drawtree | Draw tree | Yes/No | Yes
-root | Trees to be treated as Rooted | Yes/No | No
-progress | Print indications of progress of run | Yes/No | No
-[no]printsets | Print out the sets of species | Yes/No | Yes
Advanced qualifiers | Allowed values | Default
(none)

## Input file

Must be in New Hampshire standard form.

## 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