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

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

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

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

Prior and posterior distributions of parameter estimations from the Ebola phylogeny.

<p>We show the results for two different inference methods: ABC-LASSO (in red) and BEAST2-BDEI (in black). Gray distributions correspond to the prior and red distributions correspond to ABC-LASSO posterior distributions. The dots represent the median and the vertical lines represent the 95% highest posterior density of each distribution. Statistics on the BEAST2-BDEI posterior distributions were obtained from [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1005416#pcbi.1005416.ref008" target="_blank">8</a>].</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