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

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

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

HMM/HMM comparison of new domain families <i>vs.</i> Pfam-B domain families.

<p>Each point is associated with one of our HMMs and corresponds to the best alignment found between this HMM and all Pfam-B HMMs. The x-axis shows the overlap ratio of the local alignment between the two HMMs; the y-axis indicates the negative log. of the alignment p-value; blue line corresponds to <i>y</i> = −<i>log</i>(10⁻¹⁰); while the red line corresponds to <i>x</i> = 0.8.</p

Simulated phylogenies of 100 leaves assuming a BD model and their corresponding LTT plot.

<p>The red phylogeny was simulated assuming <i>θ</i> = (<i>R</i>₀ = 10, <i>d</i>_<i>I</i> = 5, <i>p</i> = 0.5) and the blue phylogeny was simulated assuming <i>θ</i> = (<i>R</i>₀ = 2, <i>d</i>_<i>I</i> = 5, <i>p</i> = 0.5). Different <i>R</i>₀s lead to different LTT plots and different tree shapes.</p