Mahesh Panchal's Homepage at the University of Reading

Software

My Programs

Here are links to the software I have written as part of my research.

NOTE: Please check your results using the summary file. The software is not appropriate with all types of data. Assumptions that are incorporated as default need to be assessed. This software allows exploratory analysis, even if certain assumptions are not met.

Automated Nested Clade Analysis v1.0 This is a fully automated version of Nested Clade Analysis. It uses TCS v1.18 (newer release available), Geodis v2.2 (newer release available), and the inference key dated 14th July 2004 (newer version available). The software is documented in Panchal (2007. Bioinformatics, 23:509-510), and is used to test the false positive rate (Panchal and Beaumont, Evolution, 61(6): 1466-1480). This software still requires commenting and adequate documentation (user guide is included). Send me an email if you wish to be kept informed.
Please remember to cite TCS and GeoDis as well. They are programmed by David Posada (http://darwin.uvigo.es).

Automated Nested Clade Analysis v1.1 This is a fully automated version of Nested Clade Analysis. It uses TCS v1.18 (newer release available), Geodis v2.2 (newer release available), and the inference key dated 11th November 2005. Please consult the user guide within to assist you in using ANeCA. Send me an email if you wish to be kept informed.
Please remember to cite TCS and GeoDis as well. They are programmed by David Posada (http://darwin.uvigo.es).

Automated Nested Clade Analysis v1.2 This version of ANeCA includes TCS v2.1 and GeoDis v2.5. An update was made to the automated inference key regarding question 19 and 20. Before, locations within the area of a subclade were considered as within the area being examined. They are now excluded.
Please remember to cite TCS and GeoDis as well. They are programmed by David Posada(http://darwin.uvigo.es).

Article: THE AUTOMATION AND EVALUATION OF NESTED CLADE PHYLOGEOGRAPHIC ANALYSIS Availability: Please email me for a copy or visit the Evolution journals website.
Abstract: Nested Clade Phylogeographic Analysis (NCPA) is a popular method for reconstructing the demographic history of spatially distributed populations from genetic data. Although some parts of the analysis are automated, there is no unique and widely followed algorithm for doing this in its entirety, beginning with the data, and ending with the inferences drawn from the data. This article describes a method that automates NCPA, thereby providing a framework for replicating analyses in an objective way. To do so a number of decisions need to be made so that the automated implementation is representative of previous analyses. We review how the NCPA procedure has evolved since its inception and conclude that there is scope for some variability in the manual application of NCPA. We apply the automated software to three published datasets previously analyzed manually and replicate many details of the manual analyses, suggesting that the current algorithm is representative of how a typical user will perform NCPA.We simulate a large number of replicate datasets for geographically distributed, but entirely random-mating, populations. These are then analyzed using the automated NCPA algorithm. Results indicate that NCPA tends to give a high frequency of false positives. In our simulations we observe that 14% of the clades give a conclusive inference that a demographic event has occurred, and that 75% of the datasets have at least one clade that gives such an inference. This is mainly due to the generation of multiple statistics per clade, of which only one is required to be significant to apply the inference key.We survey the inferences that have been made in recent publications and show that the most commonly inferred processes (Restricted Gene Flow with Isolation by Distance and Contiguous Range Expansion) are those that are commonly inferred in our simulations. However, published datasets typically yield a richer set of inferences with NCPA than obtained in our random-mating simulations, and further testing of NCPA with models of structured populations is necessary to examine its accuracy.
Status: Evolution, 61(6):1466-1480.

Favourite Software

These following links are to personally favoured software I generally use as part of my work or for fun. Some software may still be in development and most are free. There may be better commercial software out there, but I find these just as good for whatever I need to do.

Mozilla Firefox An excellent developing web browser, with tabbed windows, pop-up blocker and more.

Mozilla Thunderbird A developing stand alone e-mail client, with junk-mail filter, mail search and more.

Crimson Editor An simple text editor, with syntax-highlighting support for lots of different languages, such as Java, C, Perl, and many more. It's small and fast, and packed with features like recording macros.

Cygwin For those who use Windows but also like the Unix/Linux environment, this handy emulator saves switching computers or rebooting into a new operating system.

XFig An absolutely fantastic vector graphics package, that probably has the most awkward user-interface if you are not used to it. With a bit of practice, diagrams and the like are extreamly quick and are easily exported for use with Latex/TeX. I use the version in Cygwin.

GIMP An excellent image manipulation program that competes with the best. It has an unfamiliar interface, but is still just as powerful once you're familiar with it. It's website has a range of documentation, which is great if you're ever stuck.

MiKTeX A Windows based implementation of TeX. TeX is a typesetting system, that is great for creating professional looking documents, especially those with a great deal of mathematics. (Much better than Word when you don't really want to spend time formatting your document and the equation editor isn't upto scratch.)

Ghostscript An interpreter for the PostScript language.

Java Development Kit 1.5 The tools for compiling and running your Java programs.

ActivePerl The Perl language tools for Windows.

Knoppix Knoppix is a Linux distribution that is contained entirely on one CD. There is no need to install it since it runs off the CD too. Best of all it copies nothing to your hard disk, and can allow you to boot directly from the CD if your BIOS settings are set to boot from CD. It has various programs contained within it, and is great for starting out with if you're unfamiliar with Linux.