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
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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Last updated 6 feb 2013 jhw