Phylip : clique - Compatibility Program (Felsenstein)

your e-mail

( = required, = conditionally required)

Input File : please enter either :

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

Clique options

Bootstrap options

Output options

Other options

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Clique options

Use ancestral states in input file (A)

Specify minimum clique size? (C)

Minimum clique size



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Bootstrap options

Analyze multiple data sets (M)

How many data sets

Compute a consensus tree



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Output options

Print out compatibility matrix (3)

Print out tree (4)

Write out trees onto tree file (5)

Print out the data at start of run (1)

Indent treefile



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Other options

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



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your e-mail

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Some explanations about the options

Main parameters

Input File

Example input file

5 6

Alpha 110110

Beta 110000

Gamma 100110

Delta 001001

Epsilon 001110

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)

Clique options

Use ancestral states in input file (A)

There should also be, in the input file after the numbers of species and characters, an A on the first line of the file. There must also be, before the character data, a line or lines giving the ancestral states for each character. It will look like the data for a species (the ancestor). It must start with the letter A in the first column. There then follow enough characters or blanks to complete the full length of a species name (e. g. ANCESTOR). Then the states which are ancestral for the individual characters follow. These may be 0, 1 or ?, the latter indicating that the ancestral state is unknown.

Examples:

ANCESTOR 0010011

Minimum clique size

This option indicates that you wish to specify a minimum clique size and print out all cliques (and their associated trees) greater than or equal to than that size.

Output options

Print out tree (4)

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

Write out trees onto tree file (5)

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).