Additional file 1: of MIA: Mutual Information Analyzer, a graphic user interface program that calculates entropy, vertical and horizontal mutual information of molecular sequence sets

Drosophila-Adh data. (XLSX 153 kb

Empirical cumulative distributions and expected cumulative distributions of the simulated sequences ensemble.

<p>Vertical dotted line indicates the mean value. Panels (<b>a</b>) and (<b>b</b>) display the ECD of the full tree against the expected cumulative Poisson distribution with mean branch length <i>λ =</i> 7.01 and the expected cumulative Poisson mixture, respectively. Panel (<b>c</b>) displays the ECD of the ingroup against the expected cumulative Poisson distribution with mean branch length <i>λ =</i> 5.75. Panel (<b>d</b>) displays the ECD of the outgroup against the expected cumulative Poisson distribution with mean branch length <i>λ =</i> 25.18.</p

PKS test for strict clock on the simulated data (9 taxa) (1,000 trees, <i>k</i> = 0.50).

<p>PKS test for strict clock on the simulated data (9 taxa) (1,000 trees, <i>k</i> = 0.50).</p

PKS test for strict clock on Sanson <i>et al</i>. [36] data (16 taxa) (1,000 trees, <i>k</i> = 0.50).

<p>PKS test for strict clock on Sanson <i>et al</i>. [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0190826#pone.0190826.ref036" target="_blank">36</a>] data (16 taxa) (1,000 trees, <i>k</i> = 0.50).</p

Two-sample KS test for relaxed clock on three data-sets (<i>ENV</i> and <i>COX1</i> with 9 taxa and 18S rDNA with 17 taxa) of real sequences (1,000 trees, <i>k</i>_<i>U</i> = 0.192, <i>k</i>_<i>C</i> = 0.099).

<p>Two-sample KS test for relaxed clock on three data-sets (<i>ENV</i> and <i>COX1</i> with 9 taxa and 18S rDNA with 17 taxa) of real sequences (1,000 trees, <i>k</i>_<i>U</i> = 0.192, <i>k</i>_<i>C</i> = 0.099).</p

The 18S rDNA phylogeny of Ascomycetes.

<p>Taxa and accession numbers are: <i>Schizosaccharomyces pombe</i> (CU329672.1), <i>Lachancea waltii</i> (X89527), <i>Wickerhamomyces canadensis</i> (AB054565.1), <i>Eremothecium gossypii</i> (AY046265.1), <i>Zygosaccharomyces rouxii</i> (AY227011.1), <i>Kluyveromyces lactis</i> (HM009311.1), <i>Vanderwaltozyma polyspora</i> (JQ698890.1), <i>Nakaseomyces bacillisporus</i> (AY046252.1), <i>Nakaseomyces delphensis</i> (AY198400.1), <i>Candida glabrata</i> (KT229542.1), <i>Naumovozyma castellii</i> (HE576754), <i>Candida castellii</i> (AY046253.1), <i>Saccharomyces bayanus</i> (AY046227), <i>Saccharomyces cerevisiae</i> (JQ409454.1), <i>Saccharomyces paradoxus</i> (BR000309.1), <i>Lachancea kluyveri</i> (Z75580.1), <i>Lachancea thermotolerants</i> (CU928180.1).</p

The “nine-taxon tree” used to evolve the simulated nucleotide sequences.

<p>Dataset of simulated sequences containing 9 sequences with 10,000 nucleotides each, using the Kimura 2-Parameter (K2P) nucleotide substitution model [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0190826#pone.0190826.ref038" target="_blank">38</a>] to evolve the sequences.</p

The <i>COX1</i> phylogeny of Primates.

<p>Taxa and accession numbers are: <i>Homo sapiens</i> (YP003024028.1), <i>Pan troglodytes</i> (NP008188.1), <i>Pan paniscus</i> (NP008201.1), <i>Gorilla gorilla</i> (YP002120661.1), <i>Pongo abelii</i> (NP007837.1), <i>Nomascus leucogenys</i> (YP008379101.1), <i>Macaca fascicularis</i> (YP002884228.1), <i>Mus musculus</i> (NP904330.1).</p

Empirical cumulative distributions and 99% confidence bands for the three data-sets of real sequences.

<p>The confidence band (the two black curves) is constructed around the ECD of the unconstrained ensemble. In the <i>COX1</i> and 18S rDNA, the blue curve is underneath the red curve.</p

Two-sample KS tests for strict and relaxed clock on Padovan <i>et al</i>. [37] data (134 taxa) (15,000 trees, <i>k</i>_<i>U</i> = 0.04, <i>k</i>_<i>C</i> = 0.19 (strict clock), <i>k</i>_<i>C</i> = 0.05 (relaxed clock)).

<p>Two-sample KS tests for strict and relaxed clock on Padovan <i>et al</i>. [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0190826#pone.0190826.ref037" target="_blank">37</a>] data (134 taxa) (15,000 trees, <i>k</i>_<i>U</i> = 0.04, <i>k</i>_<i>C</i> = 0.19 (strict clock), <i>k</i>_<i>C</i> = 0.05 (relaxed clock)).</p