TIGER: Identifying rapidly-evolving characters in evolutionary data.

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.

In this video, Prof. James McInerney outlines the theory behind TIGER and the possible uses for the program.

You can download the UNIX/MACOSX version here:

You can download the Windows version here:

***UPDATE***** AS OF 3RD MAY 2016 WE HAVE DISCOVERED A BUG THAT MIS-CALCULATES THE RATES OF SOME SITES IN SOME CASES. WE ARE WORKING ON FINDING THE BUG AND PRODUCING A BUG-FREE VERSION, THEREFORE WE RECOMMEND YOU PROCEED WITH CAUTION WITH THE CURRENT VERSION.

 

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?

Implementing and testing the multispecies coalescent model: a valuable paradigm for phylogenomics
SV Edwards, Z Xi, A Janke, BC Faircloth - Molecular Phylogenetics …, 2015

Estimating phylogenetic trees from discrete morphological data
AM Wright - 2015 - repositories.lib.utexas.edu

Spiralian phylogeny informs the evolution of microscopic lineages
CE Laumer, N Bekkouche, A Kerbl, F Goetz, RC Neves - Current Biology, 2015

Coalescence vs. concatenation: sophisticated analyses vs. first principles applied to rooting the angiosperms
MP Simmons, J Gatesy - Molecular phylogenetics and evolution, 2015

[HTML] Phylogenetic Signal Dissection Identifies the Root of Starfishes
R Feuda, AB Smith - 2015 - dx.plos.org

A Guide to Phylogenetic Reconstruction Using Heterogeneous Models—A Case Study from the Root of the Placental Mammal Tree
RJ Moran, CC Morgan, MJ OConnell - Computation, 2015

Advances in Geometroidea phylogeny, with characterization of a new family based on Pseudobiston pinratanai (Lepidoptera, Glossata)
H Rajaei, C Greve, H Letsch, D Stning - Zoologica …, 2015

Phylogenomic resolution of scorpions reveals multilevel discordance with morphological phylogenetic signal
PP Sharma, R Fernndez - … of the Royal …, 2015 - rspb.royalsocietypublishing.org
Automatic selection of partitioning schemes for phylogenetic analyses using iterative k-means clustering of site rates
PB Frandsen, B Calcott, C Mayer - BMC evolutionary …, 2015

A new extant family of primitive moths from Kangaroo Island, Australia, and its significance for understanding early Lepidoptera evolution
NP Kristensen, DJ Hilton, A Kallies, L Milla - Systematic …, 2015

Systematizing morphology: a total evidence approach to ditrysian phylogenetics (Lepidoptera)
M Heikkil - 2014

A new extant family of primitive moths from Kangaroo Island, Australia, and its significance for understanding early Lepidoptera evolution
NP Kristensen, DJ Hilton, A Kallies, L Milla - Systematic …, 2015

Posterior predictive Bayesian phylogenetic model selection
PO Lewis, W Xie, MH Chen, Y Fan - Systematic …, 2014

An alternative root for the eukaryote tree of life
D He, O FizPalacios, CJ Fu, J Fehling, CC Tsai - Current Biology, 2014

Coalescent versus concatenation methods and the placement of Amborella as sister to water lilies
Z Xi, L Liu, JS Rest, CC Davis - Systematic biology, 2014

Serine codon-usage bias in deep phylogenomics: pancrustacean relationships as a case study
O Rota-Stabelli, N Lartillot, H Philippe - Systematic …, 2013

Separating the wheat from the chaff: mitigating the effects of noise in a plastome phylogenomic data set from Pinus L.(Pinaceae)
M Parks, R Cronn, A Liston - BMC Evolutionary Biology, 2012 - biomedcentral.com

Early evolution without a tree of life
WF Martin - Biol Direct, 2011

An alternative root for the eukaryote tree of life
D He, O FizPalacios, CJ Fu, J Fehling, CC Tsai - Current Biology, 2014

Phylogenetics and biogeography of the Balkan 'sand gobies'(Teleostei: Gobiidae): vulnerable species in need of taxonomic revision
MPM Vanhove, AN Economou - Biological Journal of …, 2012

Reconstruction of family-level phylogenetic relationships within Demospongiae (Porifera) using nuclear encoded housekeeping genes
MS Hill, AL Hill, J Lopez, KJ Peterson, S Pomponi - PloS one, 2013

Exploration of data partitioning in an eight‐gene data set: phylogeny of metalmark moths (Lepidoptera, Choreutidae)
J Rota, N Wahlberg - Zoologica Scripta, 2012

Morphology reinforces proposed molecular phylogenetic affinities: a revised classification for Gelechioidea (Lepidoptera)
M Heikkil, M Mutanen, M Kekkonen, L Kaila - Cladistics, 2014

A method of alignment masking for refining the phylogenetic signal of multiple sequence alignments
V Rajan - Molecular biology and evolution, 2013

Coalescent versus concatenation methods and the placement of Amborella as sister to water lilies
Z Xi, L Liu, JS Rest, CC Davis - Systematic biology, 2014

Posterior predictive Bayesian phylogenetic model selection
PO Lewis, W Xie, MH Chen, Y Fan - Systematic …, 2014

Convergent evolution of ecomorphological adaptations in geographically isolated Bay gobies (Teleostei: Gobionellidae) of the temperate North Pacific
RA Ellingson, CC Swift, LT Findley - Molecular phylogenetics …, 2014

Ecology drives the distribution of specialized tyrosine metabolism modules in fungi
GH Greene, KL McGary, A Rokas - Genome biology and …, 2014

Molecular phylogeny of the Cymbellales (Bacillariophyceae, Heterokontophyta) with a comparison of models for accommodating rate variation across sites
T Nakov, EC Ruck, Y Galachyants, SA Spaulding - Phycologia, 2014

Automatic selection of partitioning schemes for phylogenetic analyses using iterative k-means clustering of site rates
PB Frandsen, B Calcott, C Mayer - BMC evolutionary …, 2015

A new genus of metalmark moths (Lepidoptera, Choreutidae) with Afrotropical and Australasian distribution
J Rota, SE Miller - ZooKeys, 2013

Advances in Geometroidea phylogeny, with characterization of a new family based on Pseudobiston pinratanai (Lepidoptera, Glossata)
H Rajaei, C Greve, H Letsch, D Stning - Zoologica …, 2015

A new extant family of primitive moths from Kangaroo Island, Australia, and its significance for understanding early Lepidoptera evolution
NP KRISTENSEN, DJ HILTON, A KALLIES - Systematic …, 2015

The phylogenetic utility of acetyltransferase (ARD1) and glutaminyl tRNA synthetase (QtRNA) for reconstructing Cenozoic relationships as exemplified by the large …
CL Owen, DC Marshall, KBR Hill, C Simon - Molecular phylogenetics and …, 2015

Phylogenomic resolution of scorpions reveals multilevel discordance with morphological phylogenetic signal
PP Sharma, R Fernndez - … of the Royal …, 2015

The assignment of Prodidactidae to Hyblaeoidea, with remarks on Thyridoidea (Lepidoptera)
L Kaila, ME Epstein, M Heikkil, M Mutanen - Zootaxa, 2013

Causes of endemic radiation in the Caribbean: evidence from the historical biogeography and diversification of the butterfly genus Calisto (Nymphalidae: Satyrinae: …
P MatosMarav, RN guila, C Pea - BMC evolutionary …, 2014

Mitochondrial data are not suitable for resolving placental mammal phylogeny
CC Morgan, CJ Creevey, MJ OConnell - Mammalian Genome, 2014

Revised systematics and higher classification of pierid butterflies (Lepidoptera: Pieridae) based on molecular data
N Wahlberg, J Rota, MF Braby, NE Pierce - Zoologica …, 2014

A Guide to Phylogenetic Reconstruction Using Heterogeneous Models—A Case Study from the Root of the Placental Mammal Tree
RJ Moran, CC Morgan, MJ OConnell - Computation, 2015

Extracting phylogenetic signals from multi-labeled gene trees and its significance for species tree construction
R Cobb, R Elhesha, JG Burleigh - Proceedings of the 5th …, 2014

Studies of phylogenetic relationships and evolution of functional traits in diatoms
T Nakov - 2014

Systematizing morphology: a total evidence approach to ditrysian phylogenetics (Lepidoptera)
M Heikkil - 2014

 

Contact Details

For questions or to report a bug please contact carlacummins@gmail.com.

Share this site using the links below.

admin
Close
Follow Us For Updates
Click to follow our social media sites