McClellan Lab Software Download Page

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 XP executable: download ; Macintosh OSX (*.sit): download ; Source code (*.zip): download

File containing information about over 500 physicochemical amino acid properties (updated Apr 06): 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.

For more information, see http://genome.cs.byu.edu/treesaap.htm

For previous versions, see http://genome.cs.byu.edu/treesaap/

NOTE: The new Windows XP executable is stored in a *.rar file, not a *.zip file. If you have trouble extracting it, try downloading WinRAR. It can be found at the following download site: http://www.rarlab.com/download.htm.

We are currently working on various Flash applications for visualizing various aspects of the TreeSAAP output. As these are completed, we will post them on this site.

DataConvert 1.0

Convert any format of DNA or protein data to formats usable in major analytical software.

Windows XP executable: download ; Macintosh OSX (*.sit): download ; Source code (*.zip): download

User manual: download

CDM 2.1 (Codon-Degeneracy Model)

Selection analysis based on expected patterns of nucleotide change among protein-coding DNA sequences. Sliding-window options. Manual forthcoming.

Windows XP executable: download ; Macintosh OSX (*.sit): download ; Source code (*.zip): download

CDSParser 1.01 (CoDing Sequence Parser)

Large genomic data set assemblage tool. Automates the organization of protein-coding DNA sequences. Ideal for quickly organizing mitochondrial and viral full proteomes.

Windows XP, Macintosh OSX, Linux/Unix (*.zip): download

For more information, see http://inbio.byu.edu/faculty/dam83/CDSParser/

A working version of SeqFind, which formats information from BLAST searches for CDSParser, will be posted here shortly.

AlignmentHelper 1.2

Automates the process of translating protein-coding DNA sequences, aligning them with either ClustalW or Muscle, and translating the results back to DNA sequences. Updated user manual forthcoming.

Windows XP, Macintosh OSX, Linux/Unix (*.zip): download

SimSeq 2.2 (Simulated Sequences)

Interactive tool for simulating protein-coding genetic variation using common input parameters and a user tree. Outputs results in Nexus format.

Windows XP (*.zip): download