Phylip : fitch - Fitch-Margoliash and Least-Squares Distance Methods (Felsenstein)

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( = required, = conditionally required)

Distances matrix File : please enter either :

1. the name of a file:
2. or the actual data here:

Method (D) ? [default] FM: Fitch-Margoliash ME: Minimum Evolution

Fitch options

Randomize options

Bootstrap options

User tree options

Output options

Indent treefile

Other options

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Fitch options

Negative branch lengths allowed (-)

Power (P)



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Randomize options

Randomize (jumble) input order (J)

Random number seed (must be odd)

Number of times to jumble



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Bootstrap options

Analyze multiple data sets (M)

How many data sets

Compute a consensus tree



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User tree options

Use User tree (default: no, search for best tree) (U)



User Tree file : please enter either :

1. the name of a file:
2. or the actual data here:

How many tree(s) in the User Tree file

Use lengths from user trees (N)



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Output options

Print out tree (3)

Write out trees onto tree file (4)

Print out the data at start of run (1)



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Other options

Outgroup species (default, use as outgroup species 1) (O)

Matrix format ? [default] Square Lower-triangular Upper-triangular

Global rearrangements (G)



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Some explanations about the options

Main parameters

enter either the name of a file or the actual data

if you are using Netscape 2.x or later, you can select a file by typing its name, or better, by selecting it with the Netscape file browser (Browse button)

OR you can type your data in the next area, or cut and paste it from another application.

(but not both)

User tree options

Use User tree (default: no, search for best tree) (U)

To give your tree to the program, you must normally put it in the alignement file, after the sequences, preceded by a line indicating how many trees you give.

Here, this will be automatically appended: just give a treefile and the number of trees in it.

How many tree(s) in the User Tree file

Give this information whenever the infile does not already contain the tree.

Fitch options

Power (P)

For the Fitch-Margoliash method, which is the default method with this program, P is 2.0. For the Cavalli-Sforza and Edwards least squares method it should be set to 0 (so that the denominator is always 1). An intermediate method is also available in which P is 1.0, and any other value of P, such as 4.0 or -2.3, can also be used. This generates a whole family of methods.

Please read the documentation (man distance).

Other options

Global rearrangements (G)

The G (global search) option causes, after the last species is added to the tree, each possible group to be removed and re-added. This improves the result, since the position of every species is reconsidered. It approximately triples the run-time of the program.

Output options

Print out tree (3)

Tells the program to print a semi-graphical picture of the tree in the outfile.

Write out trees onto tree file (4)

Tells the program to save the tree in a treefile (a standard representation of trees where the tree is specified by a nested pairs of parentheses, enclosing names and separated by commas).