TIGER
TIGER: Identifying rapidly-evolving characters in evolutionary data.
About TIGER
TIGER is open source software for identifying rapidly evolving sites (columns in an alignment, or characters in a morphological dataset). It can deal with many kinds of data (molecular, morphological etc.). Sites like these are important to identify as they are very often removed or reweighted in order to improve phylogenetic reconstruction. When a site is changing very quickly between taxa it might not hold much phylogenetic information and therefore might simply be a source of noise. Use of TIGER can (a) allow you to see the amount of rapid evolution and noise in your alignment and (b) provide a quick and easy way to remove as many of the “noisy” sites as possible.
You can download the UNIX/MACOSX version here:
You can download the Windows version here:
TIGER uses conflict between site patterns as a proxy for rapid evolution; that is, a site that does not conflict with other sites in the alignment is generally a very slowly evolving or constant site. A site with lots of conflict is considered rapidly evolving (Cummins & McInerney, Systematic Biology, 2011). TIGER rates the conflict and categorizes the sites based on the rates. In this software the categories are called bins and are user definable (see manual for further details). Bin1 will contain the constant sites and the bin with the highest number will contain the most rapidly evolving sites.
System Requirements
TIGER is implemented in Python, so it should run on most computer platforms.
For UNIX machines, a working version of Python 2.5 or 2.6 is required. On Windows machines, TIGER comes with everything it needs and requires no further installations.
Manual
The TIGER manual can be downloaded here.
Citation:
Cummins, C.A. and McInerney, J.O. (2011) A method for inferring the rate of evolution of homologous characters that can potentially improve phylogenetic inference, resolve deep divergence and correct systematic biases. Systematic Biology 60 (6) 833-844. doi: 10.1093/sysbio/syr064. [link] [pdf]
Other Phylogenetic Software:
You might also be interested in our program ModelGenerator which implements a variety of methods for selecting between alternative models of sequence evolution for amino acid and nucleotide data.
If you are interested in phylogenetic supertrees, you might wish to take a look at our program CLANN. It implements a variety of supertree methods.
Who has been using TIGER?
Title: Serine codon usage bias in deep phylogenomics: pancrustacean relationships as a case study
Author(s): Omar Rota Stabelli, Nicolas Lartillot, Hervé Philippe, and Davide Pisani
Source: Systematic Biology doi:10.1093/sysbio/sys077 (PDF)
Title: A Method of Alignment Masking for Refining the Phylogenetic Signal of Multiple Sequence Alignments
Author: Vaibhav Rajan
Source: Mol Biol Evol doi:10.1093/molbev/mss264
Title: Exploration of data partitioning in an eight-gene data set: phylogeny of metalmark moths (Lepidoptera, Choreutidae).
Author(s): Rota, J. & Wahlberg, N.
Source: Zoologica Scripta, 00, 000–000. (2012).
Title: Phylogenetics and biogeography of the Balkan sand gobies’ (Teleostei: Gobiidae): vulnerable species in need of taxonomic revision
Author(s): Vanhove Maarten P. M.; Economou Alcibiades N.; Zogaris Stamatis; et al.
Source: BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY Volume: 105 Issue: 1 Pages: 73-91 DOI: 10.1111/j.1095-8312.2011.01781.x Published: JAN 2012
Title: Early evolution without a tree of life
Author(s): Martin William F.
Source: BIOLOGY DIRECT Volume: 6 Article Number: 36 DOI: 10.1186/1745-6150-6-36 Published: JUN 30 2011
Contact Details
For questions or to report a bug please contact carlacummins@gmail.com.
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