Pipeline

The general pipeline I followed is listed next. I followed the tutorials given on the website for pre-processing of the image. There is a small screen for viewing your progress and I matched that screen to images in the given tutorials at http://www.cibiv.at/software/treesnatcher/tutorials/.

1. Screenshot of dendrogram of interest and crop to size
2. Open Image
3. Select Whole Image and Global Threshold and Rectangular I tested a lot of different values here because my image had multiple colors for each group on the dendrogram.
4. Select Locate Nodes At this point, the program was selecting incorrect nodes. It was easy enough to move and delete nodes as needed. The process was not reproducible by any means.
5. Use Add Tip I again did this section by hand as the program was not selecting tips.
6. Calculate Branches This took a few tries because of step 4 being incorrect the first few tries.
7. Toggle Newick View
8. read.tree from the ape package in R.

I snatched that tree and have no idea what to do next! Pretty easy to use program overall and I will be on the lookout for more trees that may improve prediction in my dataset…more to come!