Phylip : pars - Discrete character parsimony (Felsenstein)

your e-mail

( = required, = conditionally required)

Input File : please enter either :

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

Pars options

Randomize options

Weight options

User tree options

Bootstrap options

Output options

Parcimony options

Other options

---

Pars options

Search option (S) ? [default] More thorough search Rearrange on one best tree Less thorough

Number of trees to save? (V)

Use ancestral states in input file (A)



[Return to the main part with your favorite browser's Back function]

---

Randomize options

Randomize (jumble) input order (J)

Random number seed (must be odd)

Number of times to jumble



[Return to the main part with your favorite browser's Back function]

---

Weight options

Weighted sites (W)



Weight file : please enter either :

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

[Return to the main part with your favorite browser's Back function]

---

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



[Return to the main part with your favorite browser's Back function]

---

Bootstrap options

Analyze multiple data sets (M)

How many data sets

Random number seed (must be odd)

Number of times to jumble

Compute a consensus tree



[Return to the main part with your favorite browser's Back function]

---

Output options

Print out tree (3)

Print out steps in each character (4)

Print states at all nodes of tree (5)

Write out trees onto tree file (6)

Print out the data at start of run (1)

Indent treefile



[Return to the main part with your favorite browser's Back function]

---

Parcimony options

Use Threshold parsimony (T)

Threshold value (if use threshold parsimony)



[Return to the main part with your favorite browser's Back function]

---

Other options

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



[Return to the main part with your favorite browser's Back function]

---

your e-mail

---

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.

Pars options

Search option (S)

PARS is a general parsimony program which carries out the Wagner parsimony method with multiple states. Wagner parsimony allows changes among all states. The criterion is to find the tree which requires the minimum number of changes. The Wagner method was originated by Eck and Dayhoff (1966) and by Kluge and Farris (1969). Here are its assumptions:

1. Ancestral states are unknown.

2. Different characters evolve independently.

3. Different lineages evolve independently.

4. Changes to all other states are equally probable (Wagner).

5. These changes are a priori improbable over the evolutionary time spans involved in the differentiation of the group in question.

6. Other kinds of evolutionary event such as retention of polymorphism are far less probable than these state changes.

7. Rates of evolution in different lineages are sufficiently low that two changes in a long segment of the tree are far less probable than one change in a short segment.

PARS can handle both bifurcating and multifurcating trees. In doing its search for most parsimonious trees, it adds species not only by creating new forks in the middle of existing branches, but it also tries putting them at the end of new branches which are added to existing forks. Thus it searches among both bifurcating and multifurcating trees. If a branch in a tree does not have any characters which might change in that branch in the most parsimonious tree, it does not save that tree. Thus in any tree that results, a branch exists only if some character has a most parsimonious reconstruction that would involve change in that branch.

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

Weight options

Weighted sites (W)

The weights follow the format described in the main documentation file, with integer weights from 0 to 35 allowed by using the characters 0, 1, 2, ..., 9 and A, B, ... Z.

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).