Phylip
: dnapars (Felsenstein)
your e-mail
(
= required,
= conditionally required)
Alignement File : please enter
either
:
the name of a
file
:
or
the
actual data
here:
Input sequences
interleaved
(I)
Parcimony options
Randomize options
Bootstrap options
User tree options
Output options
Other options
Parcimony options
Use Threshold parsimony (T)
Threshold value (if use threshold parsimony)
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Randomize options
Randomize (jumble) input order (J)
Random number seed (must be odd) (if randomize)
Number of times to jumble (if randomize)
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Bootstrap options
Perform a bootstrap before analysis
Bootstrap
Delete-half jackknife
Permute species for each character
Resampling methods
Random number seed
How many replicates
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
:
the name of a
file
:
or
the
actual data
here:
How many tree(s) in the User Tree file
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Output options
Print out tree (3)
Print out steps in each site (4)
Print sequences at all nodes of tree (5)
Write out trees onto tree file (6)
Print out the data at start of run (1)
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Other options
Outgroup species (default, use as outgroup species 1) (O)
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your e-mail
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)
Input sequences interleaved (I)
In 'sequential' format, you give all of the data for the first species, then all of the characters for the next species, and so on.
In 'interleaved' format, sequences are given aligned, with some lines giving the first part of each of the sequences, then lines giving the next part of each, and so on.
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.
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).
Bootstrap options
Resampling methods
1. The bootstrap. Bootstrapping was invented by Bradley Efron in 1979, and its use in phylogeny estimation was introduced by me (Felsenstein, 1985b). It involves creating a new data set by sampling N characters randomly with replacement, so that the resulting data set has the same size as the original, but some characters have been left out and others are duplicated. The random variation of the results from analyzing these bootstrapped data sets can be shown statistically to be typical of the variation that you would get from collecting new data sets. The method assumes that the characters evolve independently, an assumption that may not be realistic for many kinds of data.
2. Delete-half-jackknifing. This alternative to the bootstrap involves sampling a random half of the characters, and including them in the data but dropping the others. The resulting data sets are half the size of the original, and no characters are duplicated. The random variation from doing this should be very similar to that obtained from the bootstrap. The method is advocated by Wu (1986).
3. Permuting species within characters. This method of resampling (well, OK, it may not be best to call it resampling) was introduced by Archie (1989) and Faith (1990; see also Faith and Cranston, 1991). It involves permuting the columns of the data matrix separately. This produces data matrices that have the same number and kinds of characters but no taxonomic structure. It is used for different purposes than the bootstrap, as it tests not the variation around an estimated tree but the hypothesis that there is no taxonomic structure in the data: if a statistic such as number of steps is significantly smaller in the actual data than it is in replicates that are permuted, then we can argue that there is some taxonomic structure in the data (though perhaps it might be just a pair of sibling species).
Form generator version: 3.a (11 Mar 1998 19:05)