Difference between revisions of "Creating Tree Files"
From phenoscape
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The following are instructions for creating and saving trees using [http://mesquiteproject.org/mesquite/mesquite.html Mesquite]. You should have a [http://sourceforge.net/ SourceForge] account and access to the [[Data_Repository_Access_Instructions|Phenoscape Data Repository]] before beginning. | The following are instructions for creating and saving trees using [http://mesquiteproject.org/mesquite/mesquite.html Mesquite]. You should have a [http://sourceforge.net/ SourceForge] account and access to the [[Data_Repository_Access_Instructions|Phenoscape Data Repository]] before beginning. | ||
| − | + | You might begin with an existing nexus file containing the data matrix for the publication, or create a new nexus file containing a list of matrix taxa copied from the Matrix Taxon column in Phenex. | |
| − | # | + | |
| − | + | # Open nexus file in Mesquite. You should see the data matrix wth list of taxa in the left-hand column. | |
| + | # Next, create a Tree Block (which will contain one or more trees for the publication) by selecting Taxa&Trees > New Empty Block of Trees. Click OK if Mesquite asks for Name of trees block. | ||
| + | # Click on the “View Trees” icon below “Trees” on the left hand side of the Mesquite window. You may need to click on the arrow to display the tree icons. | ||
| + | ## A ”default bush” tree will appear. | ||
| + | # Optional: format the tree display to make it easier to read names manipulate the tree | ||
| + | ## go to Drawing > Tree Form > Square Tree | ||
| + | ## go to Drawing > Orientation > Right | ||
| + | ## go to Drawing > Set Current Orientation as Default | ||
| + | # Modify the tree as needed to replicate the publication tree | ||
| + | # Store the tree by going to Tree>Store Tree As | ||
| + | ## Name the tree after the figure number (e.g., Figure 6.). | ||
| + | # To add additional trees to the file, modify the current tree (e.g., Figure 6) as needed, then go to Tree > Store Tree As | ||
| + | ## Name the tree after the new figure number | ||
[[Category:Curation]] | [[Category:Curation]] | ||
Revision as of 22:15, 10 February 2009
The following are instructions for creating and saving trees using Mesquite. You should have a SourceForge account and access to the Phenoscape Data Repository before beginning.
You might begin with an existing nexus file containing the data matrix for the publication, or create a new nexus file containing a list of matrix taxa copied from the Matrix Taxon column in Phenex.
- Open nexus file in Mesquite. You should see the data matrix wth list of taxa in the left-hand column.
- Next, create a Tree Block (which will contain one or more trees for the publication) by selecting Taxa&Trees > New Empty Block of Trees. Click OK if Mesquite asks for Name of trees block.
- Click on the “View Trees” icon below “Trees” on the left hand side of the Mesquite window. You may need to click on the arrow to display the tree icons.
- A ”default bush” tree will appear.
- Optional: format the tree display to make it easier to read names manipulate the tree
- go to Drawing > Tree Form > Square Tree
- go to Drawing > Orientation > Right
- go to Drawing > Set Current Orientation as Default
- Modify the tree as needed to replicate the publication tree
- Store the tree by going to Tree>Store Tree As
- Name the tree after the figure number (e.g., Figure 6.).
- To add additional trees to the file, modify the current tree (e.g., Figure 6) as needed, then go to Tree > Store Tree As
- Name the tree after the new figure number
