TreeSAAP 3.2 (Selection on Amino Acid Properties)
Detailed analysis of selection on amino acid properties using user-defined phylogenetic trees. Sliding-window options. Manual forthcoming.
Windows executable: download ; Macintosh OSX (*.sit): download ; Linux (*.tgz) code; download
Source code (*.zip): downloadFile containing 539 physicochemical amino acid properties (updated Apr 2008): download
NOTE: This document can be edited to add to or subtract from the list of available amino acid properties by simply opening the file in a spreadsheet program and saving the result as a tab-delimited text file. To download, right click on the download link above and save the target to your computer. Use it to replace the text file ’31 Properties.txt’ found in TreeSAAP\Data\PROTEIN_PROPERTIES\ wherever TreeSAAP is installed on your computer.
You should look through the following tutorials:
The following videos demonstrate usage of TreeSAAP from start to finish:
- Video on how to use MEGA to create files for use in TreeSAAP
- Video on how to use TreeSAAP once you have data
- demo.fas - FASTA file containing unaligned sequences
- demo.mas - 'MEGA Alignment Session' file
- demoaligned.fas - FASTA file containing aligned sequences. Used to create input for TreeSAAP.
- demo.meg - MEGA session
- demoTree.nwk - Newick export of the phylogenetic tree. Used to create input for TreeSAAP.
- demonotNewickTree.mts - Saved MEGA tree
- treeSAAPfile.txt - Input for TreeSAAP
- Final Excel Document - Final document showing analysis for the amino acid property 'Power to be at the N-Terminus'