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)
-
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.
- User Tree file
- Give a tree whenever the infile does not already contain the tree.
- How many tree(s) in the User Tree file
- Give this information whenever the infile does not already contain the tree.
-
-
Mix options
- Use Mixed method (X)
- You have to put on the first line of the input file, after the number of species and the number of characters, the character M, to signal that the Mixture information follows. There then follows, before the species data, a line or lines, the first character the first line being M. There then follow as many characters as are needed to fill out the length of a species name, and one letter for each for each character. These letters are C or S if the character is to be reconstructed according to Camin-Sokal parsimony, W or ? if the character is to be reconstructed according to Wagner parsimony. So if there are 20 characters the line giving the mixture might look like this:
- Mixture WWWCC WWCWC
- Parsimony method (P)
- Only if Use Mixed method is disabled.
- 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
-
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 (6)
- 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).
References:
Felsenstein, J. 1993. PHYLIP (Phylogeny Inference Package) version 3.5c. Distributed by the author. Department of Genetics, University of Washington, Seattle.
Felsenstein, J. 1989. PHYLIP -- Phylogeny Inference Package (Version 3.2). Cladistics 5: 164-166.
Pise form generator version: 5.a (19 Oct 2006 12:42)