Rate estimation accuracy is highly dependent on the simulated indel rate.

<p>For instance, PRANK is more accurate at lower indel rates, ProbCons is more accurate at higher rates. ProtPal is more accurate than PRANK in all but one rate (0.005) and equal or more accurate than ProbCons in all but one rate (0.08). The drift towards exhibited by most programs indicates that most programs infer proportionally fewer indels as rates are increased, likely due to various forms of gap attraction. Color-coded 90% quantiles and RMSEs are shown underneath and to the right of each group of distributions, respectively. RMSE is computed as described in 1 Equation 1.</p

Each path through this state graph represents a possible evolutionary history relating sequences GL and GIV.

<p>By using stochastic traceback algorithms (sampling paths proportional to their posterior probability, blue highlighted states and transitions), it is possible to select a high-probability subset of the full state graph. By constructing such a subset at each internal node, it is possible to maintain a bound on the state space size during progressive tree traversal while still retaining an ensemble of possible histories.</p

Additional file 1: of TrawlerWeb: an online de novo motif discovery tool for next-generation sequencing datasets

Table S1. Details of the assessment of TrawlerWeb. Detailed table of Fig. 1b showing, for each ChIP experiment, the ability of individual programs to uncover the correct binding site in yeast. For each individual ChIP experiment, the success or failure of 8 different algorithms including TrawlerWeb is shown. The results from the 6 algorithms (Coverage, AlignACE, Kellis, mdscan, MEME, and MEME-c) were extracted from Harbison et al. 2004 [38]. The matching motifs found by TrawlerWeb are identical to that found by Trawler_standalone (detailed previously in Ettwiller et al. 2007 [5]). The results from RSAT were performed by this study, where the matching motifs found by RSAT were described in the last column. (XLSX 190 kb

Additional file 2: of TrawlerWeb: an online de novo motif discovery tool for next-generation sequencing datasets

Table S2. Details of motif occurrence comparison between web-based motif discovery software. The highest scoring motifs discovered in DREME, MEME, RSAT peak-motifs, and TrawlerWeb and their corresponding occurrences are illustrated here. For the highest scoring motif, the number of motif occurrences were expressed as a percentage of the total number of input sequences. *MEME-ChIP pre-processes submitted sequences longer than 100 by trimming them evenly from both ends to get the centered 100 bp sequence and discards trimmed sequences containing only Ns from repeat masking. **MEME motif discovery automatically limits the run to a randomly sampled 600 sequences to reduce run time. (XLSX 576 kb