Comparison of performances between ACO-ME and hill-climbing (with and without Steepest Descent, SD) after a fixed run time of 1 minute on datasets of 55 (a) and 500 (b) taxa

<p><b>Copyright information:</b></p><p>Taken from "An ant colony optimization algorithm for phylogenetic estimation under the minimum evolution principle"</p><p>http://www.biomedcentral.com/1471-2148/7/228</p><p>BMC Evolutionary Biology 2007;7():228-228.</p><p>Published online 15 Nov 2007</p><p>PMCID:PMC2211314.</p><p></p> A paired Wilcoxon test indicates that ACO-ME performances are significantly better (-value = 3.92for 55 taxa dataset, and -value = 6.821for 500 taxa dataset) than those of hill-climbing with SD, but significantly worst (-value = 4.71for 55 taxa dataset, and -value = 4.53for 500 taxa dataset) than those of hill-climbing without SD

Schematic of the "ancestral sequence tree" method used for inferring the phylogeny among putative toxins sequences uncovered by TAQ V1

0. In this hypothetical example, the sequences are separated into 4 groups. Black edges represent the ML phylogenies within each of the 4 considered groups. The red dots stand for the inferred ancestral sequence of each group. The red edges define the phylogeny among the inferred ancestral sequences. Schematic of the second heuristic ("super tree" approach) used for inferring the phylogeny among putative toxins sequences uncovered by TAQ V1.0. In this hypothetical example, the sequences are separated into 3 groups. The red, green, and blue trees represent the ML phylogenies within each of the 3 considered groups. These source trees are then used collectively for generating the best super tree, ., the tree including all sequences that is most compatible with all source trees (see Methods section for details).<p><b>Copyright information:</b></p><p>Taken from "Automated discovery and phylogenetic analysis of new toxin-antitoxin systems"</p><p>http://www.biomedcentral.com/1471-2180/8/104</p><p>BMC Microbiology 2008;8():104-104.</p><p>Published online 25 Jun 2008</p><p>PMCID:PMC2446400.</p><p></p

Blue and red lineages represent known and unknown TA systems, respectively

Green lineages represent sequences annotated as "containing a PIN domain".<p><b>Copyright information:</b></p><p>Taken from "Automated discovery and phylogenetic analysis of new toxin-antitoxin systems"</p><p>http://www.biomedcentral.com/1471-2180/8/104</p><p>BMC Microbiology 2008;8():104-104.</p><p>Published online 25 Jun 2008</p><p>PMCID:PMC2446400.</p><p></p

IBP microsat data

Excel file containing microsatellite data of females and the ducklings in their nest