Common LISP simulation programs

These two .zip archives contain the LISP programs that have been used in the simulation section for: (1) Yule trees and the 2-state symmetric model, (2) non-molecular-clock trees and HKY+G4 model. Readme are enclosed for further explanations

ONLINE_APPENDIX_REVISED

ONLINE_APPENDIX_REVISE

Prior table for Ebola data.

<p>Prior table for Ebola data.</p

Summary statistics based on the tree topology (topo set).

<p>Summary statistics based on the tree topology (topo set).</p

Number of domains and FDR obtained with different e-value and p-value cutoffs.

<p>This figure reports the FDRs estimated by the methods that use reverse sequences (a) and 4-mer shuffling (b).</p

HMM/HMM comparison of domains identified by our approach that overlap a known Pfam domain.

<p>The x-axis shows the overlap ratio of the local alignment; the y-axis indicates the negative log of the alignment p-value; the blue line denotes the 10⁻¹⁰ p-value, while the red line denotes the 80% overlap.</p

Similarity between GO annotations associated with domain families.

<p>Left: annotation similarity between dissimilar domain families. Right: annotation similarity between domain families identified as similar in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1005889#pcbi.1005889.g008" target="_blank">Fig 8(d)</a>.</p

Performance of the ABC-LASSO and the kernel-ABC methods on non-ultrametric trees (<i>c</i>₁ = 2).

<p>Mean Relative Error (MRE) and 95% HPD accuracy (<i>accuracy</i>_95%) of inference of the SI-DR epidemiological parameters by both ABC-LASSO and kernel-ABC approaches. For the ABC-LASSO method, we show the results obtained on the 100 large target trees (1,000 leaves) enclosed in brackets. For the kernel-ABC method, we show the results obtained after extending the MCMC chain length to 50,000 steps for 10 target trees enclosed in square brackets.</p

Quality scores measured on models obtained without co-occurrence (in blue), models obtained with co-occurrence (in red) and Pfam models (in green).

<p>(a) Homogeneity; (b) Entropy; (c) Hydrophobicity; (d) Complexity.</p

Influence of the tolerance parameter on the error for four ABC approaches used on all summary statistics.

<p>The x-axis shows the tolerance value. Squares represent the mean relative errors for each tolerance value with their standard errors. We show errors generated by ABC-D in turquoise, by ABC in blue, by ABC-FFNN in orange and by ABC-LASSO in red. The gray horizontal lines correspond to the mean relative error of the prior (i.e. expected error in rejection with a tolerance of 1). Results are displayed for both BD and SIR models and trees of both 100 leaves and 1,000 leaves.</p