Software for phylogenetic conservation analysis

Software for phylogenetic conservation analysis (Schauer et al. paper)

GENERAL

Software used for analysis of the AGL6 and AGL13 introns can be downloaded from this page. This page also includes brief instructions of use for these programs. All progams on this page were written by Philipp Schlüter. Programs were compiled as executables for Windows operating systems using Delphi 2006. Please note that by downloading you agree to the following legal disclaimer :

Legal disclaimer

All software (c) Copyright 2008 Philipp M Schlüter.
Thiese programs are distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY, whether expressed or implied; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. The author (PMS) will not be liable for any special, incidental, consequential, indirect or similar damages due to loss of data or any other reason, even if he or an agent of his has been advised of the possibility of such damages. In no event shall the author be liable for any damages, regardless of the form of the claim. The person using the software bears all risk as to the quality and performance of the software.

Software is provided as-is and free of charge. None of these programs may be included in any commercial software package without the explicit permission of the author.

Installation: Simply unzip the downloaded file and start by clicking on the .exe file. Some of the zips also include example input/output files.

Apart from the software below, you will need the following for conducting similar analyses:

1) Input sequences aligned and saved as .FAS (FASTA) files.

2) Software: For simple mismatch analysis just what is on this page, for MP (Maximum Parsimony) analysis, PAUP*, and for ML (Maximum Likelihood) analysis Modeltest and PAUP*.

SOFTWARE

To download the complete set (including documentation), click here. The documentation is also available separately here. The individual programs are listed below:

Sliding divergence sequence window (sdsw.exe): here. This program needs a set of ALIGNED FASTA format sequences (at least two; gap character '-') as input and computes pairwise mismatch values for sliding windows of a given size, with a given step size. This is done for every pair of sequences in the input file, and, in addition, average values across all pairs are calculated. Calculations are done in two ways: (a) ignoring comparisons of a nucleotide chararcter with a gap character (N/-) in the mismatch, or (b) including it (more details in the accompanying pdf). The output is written as tab-delimited text.

.FAS to .NEX converter (fas2nex.exe): here. This file can read a .FAS (FASTA) file and save it as .NEX (NEXUS) file (or again as a .fas file) for phylogenetic analysis with PAUP*, with the option of removing columns of characters consisting only of gaps. If necessary, the ends of short sequences in the .fas file will be padded to full length.

PAUP Text Generator and Parser (txgen.exe) - here. This program generates a script for PAUP*, to calculate MP or ML tree scores on a sliding window of nucleotide data given an input tree. The program also parses PAUP*'s log file into a table that can be used in your favourite spreadsheet.

Conserved Seq Window Annotater (cswA.exe) - here. This program reads a .FAS file, along with a set of scores and putative sequence elements and visually annotates the input sequence with the conservation information as well as the position (and match) of the sequence elements.

Sequence Resampler (ResampleSeq.exe) - here. This program allows you to randomly resample a set of input sequences.

The following may also be useful: Reverse/Complement (RC.exe) - here. This simple utility lets you reverse, complement or reverse-complement an input sequence.

If you want to do dotplots:

Simple Shaded DotPlotter (dotplot.exe) - here. This program allows you to do dotplot analysis and highlight selected sequence regions on the dotplot. It also provides a simple numerical evalutation of the dotplot data that can then be used for statistics.

BMP Frame (BmpFrame.exe) - here. This program allows you to draw a frame with tick marks around an 8-bit bitmap.

ALIGNMENTS

The nucleotide (cds and intron 1) and amino acid sequence alignments for the AGL6/AGL13 paper (Schauer et al.) can be downloaded here.

Contact

If you have any problems or questions regarding the software or analysis, you can reach me at firstname(dot)lastname[at]systbot(dot)uzh(dot)ch. My first and last name spelled as philipp and schlueter, respectively. For questions about other aspects of the Schauer et al. paper itself, please contact Dr. Skip Schauer or Prof. Dr. Ueli Grossniklaus.