Laboratory Notes for BIO 1016 & 3001

Enter data and run a cladistic analysis using Winclada and TNT

© Donald McClelland, 6 February 2013

We will be using the program winclada to build a matrix of taxa and characters. We will then analyze the matrix in TNT to build a phylogeny of the taxa.

Download the programs: Go to http://www.cladistics.com

Download Winclada

Download TNT: Win (menu interface)

To open Winclada

Double click file “wiclada.exe”

To build a matrix

Click Matrix > New Matrix (create)

Set size (you can always add or delete taxa and characters)

Choose NONadditive (Fitch)

To name taxa

Click Term > terminal dialog

From there you can navigate through the taxa and change the names (you can include other information, but you don’t need to).

To name characters and define states

Click Chars > Character dialog

From there you can name the character and define each state

To enter data in your matrix

You must unlock the matrix. If you try to enter data you will be asked if you want to unlock the matrix. Or you can click Edit > Unlocked – data entry allowed

The first taxon in you matrix is automatically used for rooting the tree when you analyze your data. Put your outgroup in the first position. If it isn’t already there, select it by double clicking it then

Click > Chars > Move selected character > to Beginning

To enter a polymorphism (more than one character state in a single taxon)

Click Edit > enter polymorphisms

To change the direction of movement of you cursor (down vs. to right) for easy data entry

Click View > Cursor settings

Save your matrix

Click File > Save matrix as (Nona format)

To analyze your matrix

Open TNT by double clicking “tnt.exe”

Open your matrix

Click File > open input file

Change Files of type: to “ALL files”

Select your matrix

Run analysis using TNT

Click Settings > Memory

Increase Max trees to 10000

Click Analyze > Traditional search

Change “random seed” to 0

Increase trees to save per replication to 100

If not already selected, select tree bisection reconnection (TBR)

Click Search

To save trees

Click > File > Tree save file > open parenthetical

Name your file

Click > File > Tree save file > Save trees to open file

On popup window select all trees (if not selected already) and click “OK”

Click > File > Tree save file > Close tree file

To view these trees

Open your matrix in winclada

Click > File > Open Tree file

You will probably get several trees showing up in the winClados interface

To see a consensus tree

Click Trees > Consensus compromise > Consensus (strict)

To change the tree style

Click View > Tree style

Select the style you want (I like “Rectangular style (Clados)”)

To display characters, character numbers or names, and character states

Click HashMarks > Map Characters (show hashmarks)

Click HashMarks > Number hashmarks (characters)

Click HashMarks > Number hashmarks (states)

Click HashMarks > Label hashmarks with Char-Names

To return to your matrix

Click Interface > winDada

To save a tree

File > Create Tree Metafile

Save it whereever you want

You can open this file in Adobe illustrator, PowerPoint, inkscape etc.

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