How should gaps be treated in parsimony? A comparison of approaches using simulation Export

@article{citeulike:1155314, abstract = {Simulation with indels was used to produce alignments where true site homologies in DNA sequences were known; the gaps from these datasets were removed and the sequences were then aligned to produce hypothesized alignments. Both alignments were then analyzed under three widely used methods of treating gaps during tree reconstruction under the maximum parsimony principle. With the true alignments, for many cases (82\%), there was no difference in topological accuracy for the different methods of gap coding. However, in cases where a difference was present, coding gaps as a fifth state character or as separate presence/absence characters outperformed treating gaps as unknown/missing data nearly 90\% of the time. For the hypothesized alignments, on average, all gap treatment approaches performed equally well. Data sets with higher sequence divergence and more pectinate tree shapes with variable branch lengths are more affected by gap coding than datasets associated with shallower non-pectinate tree shapes.}, author = {Ogden, Heath T. and Rosenberg, Michael S.}, citeulike-article-id = {1155314}, citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.ympev.2006.07.021}, citeulike-linkout-1 = {http://www.sciencedirect.com/science/article/B6WNH-4KPNVT3-1/2/f54f60f234abb643967c4e7a06137d3c}, doi = {10.1016/j.ympev.2006.07.021}, journal = {Molecular Phylogenetics and Evolution}, keywords = {2007, accuracy, alignments, dna, gaps, indels, parsimony, simulation}, month = {March}, number = {3}, pages = {817--826}, posted-at = {2008-11-25 11:52:53}, priority = {2}, title = {How should gaps be treated in parsimony? A comparison of approaches using simulation}, url = {http://dx.doi.org/10.1016/j.ympev.2006.07.021}, volume = {42}, year = {2007} }

TY - JOUR ID - citeulike:1155314 L3 - citeulike-article-id:1155314 N2 - Simulation with indels was used to produce alignments where true site homologies in DNA sequences were known; the gaps from these datasets were removed and the sequences were then aligned to produce hypothesized alignments. Both alignments were then analyzed under three widely used methods of treating gaps during tree reconstruction under the maximum parsimony principle. With the true alignments, for many cases (82%), there was no difference in topological accuracy for the different methods of gap coding. However, in cases where a difference was present, coding gaps as a fifth state character or as separate presence/absence characters outperformed treating gaps as unknown/missing data nearly 90% of the time. For the hypothesized alignments, on average, all gap treatment approaches performed equally well. Data sets with higher sequence divergence and more pectinate tree shapes with variable branch lengths are more affected by gap coding than datasets associated with shallower non-pectinate tree shapes. IS - 3 JF - Molecular Phylogenetics and Evolution EP - 826 TI - How should gaps be treated in parsimony? A comparison of approaches using simulation VL - 42 SP - 817 KW - 2007 KW - accuracy KW - alignments KW - dna KW - gaps KW - indels KW - parsimony KW - simulation AU - Ogden, Heath AU - Rosenberg, Michael PY - 2007/03// UR - http://dx.doi.org/10.1016/j.ympev.2006.07.021 ER -