Instructions

Fill in the five sections of the form below:
Within each section, alternatives are in different coloured rows.
Where necessary, the alternatives have various fields to be filled out.
Press 'Submit Form' - a PAUP command-file will be e-mailed to the address you provide, along with some instructions on how to run the search.

1. Basic Details

First name:
Last name:
E-mail:
	This is required - the PAUP command-file will be e-mailed to you. This data will not be passed on to third parties. The size of the PAUP command-file produced depends on the options picked. The largest file size is about 4Mb (most are much, much smaller).

2. Character Base-Weights

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Both search strategies in Section 4 use alternating phases of normally-weighted and reweighted characters.
This section determines the base-weights for your data - this will be used in the normally-weighted phases.

Equal-weights	This will give all characters a weight of '1'. Use this if you are unsure about weights.
Use the weight-set called
	This will use the weights you define in a PAUP weight-set (see PAUP's own instructions on how to do this). Undefined characters will be given a default weight of '1'.

3. Initial Search (for starter-trees)

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Both search strategies in Section 4 need to start with some trees in memory - they use this as a jumping-off point to search for better trees.
If you don't already have some trees saved from an earlier search, you need to run a heuristic search to find some.
There is obviously a trade-off between the time spent on this search versus the quality of your starter-tree - the decision has to be yours, I'm afraid!
A tip - the 'New Strategy' benefits more from better starter-trees that the 'Parsimony Ratchet'.

None	You must have your own starter-trees already in PAUP.
Heuristic Search
Number of Reps:		(usually 100-1000)
Holding:		trees at each step (usually 1-10)
Search limit:		None

4. Main Search (for MPTs)

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This sections implements the main part of your search.
There are no hard-and-fast rules about which search is best, or what settings to use - you must decide!
You need to balance, for example, the time spent on the search against the probability of finding the shortest trees.
A tip - the default settings are a reasonable starting point!

Nixon 1999 'Parsimony Ratchet' (popup about the 'Parsimony Ratchet'...)
Number of Characters:	(max. 5,000) Event-pairs (max. 11,175)
	Set this to the total number of characters in your data-set. 'Event-pairs' resamples sets of EP-characters, assuming PAUP charsets called 'Event_1', 'Event_2'... etc. If you don't know what event-pairs are, don't check this option!
Number of Reps:	(usually 50-1,000; max. 2,000)
Holding:	MPTs between each rep (usually 1-10)
	A larger value will assess more trees in each rep, but the search will run much slower.
Reweighting:	percent of characters given a weight of
	This will be rounded down to nearest whole number of characters.
Search limit:	None
Final Branch-swap:		A final branch-swap will add time, but could find more trees.
Quicke et al 2001 'New Strategy' (popup about the 'New Strategy'...)
Reweight using:	of characters
Holding:	MPTs between each rep (usually 1-10)
	A larger value will assess more trees in each rep, but the search will run much slower.
Search limit:	None for each rep
Max. Number of Reps:		This value is the maximum number of reps you want (max. 2000). Hopefully your search will stabilise before this point!

5. Final Phase

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This section automates the process of generating consensus trees from the MPTs found by your search.

Save Consensus Trees:

Strict
Semi-Strict
Adams
Majority-rule percent
Reduced Consensus

Supplement: Techy Stuff

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This section allows you to alter the way the PAUP command-file is written and e-mailed.
Ignore it unless you are having difficulties!

Line Breaks:		Macs, PCs and Unix use a different code for line-breaks in text. PAUP should be able to run files with any type of line-break, although PAUP's text-editor can't. If you are unsure, leave on 'Mac'.
Encoding:		This sets the ways your NEXUS file is attached to the e-mail. You can probably ignore this setting, but if you are having troubles opening the attachment or running it in PAUP, you might try playing with this setting.

1. Basic Details

First name:

Last name:

E-mail:

2. Character Base-Weights

Equal-weights

Use the weight-set called

3. Initial Search (for starter-trees)

None

Heuristic Search

Number of Reps:

Holding:

Search limit:

4. Main Search (for MPTs)

Nixon 1999 'Parsimony Ratchet' (popup about the 'Parsimony Ratchet'...)

Number of Characters:

Number of Reps:

Holding:

Reweighting:

Search limit:

Final Branch-swap:

Quicke et al 2001 'New Strategy' (popup about the 'New Strategy'...)

Reweight using:

Holding:

Search limit:

Max. Number of Reps:

5. Final Phase

Save Consensus Trees:

Supplement: Techy Stuff

Line Breaks:

Encoding:

Instructions

Popup with details of this website

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