Universal Common Ancestor (UCA) test

This page contains information about our critical analyses of the UCA versus Independent Origins (IO) hypothesis testing developed by Douglas Theobald in the paper "A formal test of the theory of universal common ancestry" (Nature 2010; 465:219--222 doi:10.1038/nature09014)

Reference

Leonardo de Oliveira Martins, David Posada. Proving universal common ancestry with similar sequences Trends in Evolutionary Biology 2012, 4(1):e5 DOI: 10.4081/eb.2012.e5

Simulations and programs developed

[directory archived in tar format (1.7MB)] : These are the scripts we created for comparing alignments simulated under UCA or IO.

The analyses were conducted on a GNU/Linux cluster, but the results can be easily reproduced in a UNIX/Linux workstation without modifications - provided you have all the software described below and some familiarity with them. The R scripts needed to reproduce the figures are also included.


Software needed to run the simulations

Do CB, Mahabhashyam MSP, Brudno M, and Batzoglou S. PROBCONS: Probabilistic Consistency-based Multiple Sequence Alignment. Genome Research 15: 330-340 (2005) doi:10.1101/gr.2821705
Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL. BLAST+: architecture and applications. BMC Bioinformatics 10: 421 (2009) doi:10.1186/1471-2105-10-421
Fletcher, W. and Yang, Z. INDELible: a flexible simulator of biological sequence evolution. Mol. Biol. Evol. 26:1879-1888 (2009)
Edgar, R.C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32:1792-1797 (2004)
Other software (standard in Linux): python, biopython, R (for plotting)

This document last modified Tuesday May 15, 2012

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