@article {1149,
	title = {A Parallel and Sensitive Software Tool for Methylation Analysis on Multicore Platforms.},
	journal = {Bioinformatics (Oxford, England)},
	volume = {31},
	number = {19},
	year = {2015},
	month = {2015 Jun 10},
	pages = {3130-3138},
	abstract = {MOTIVATION: DNA methylation analysis suffers from very long processing time, since the advent of Next-Generation Sequencers (NGS) has shifted the bottleneck of genomic studies from the sequencers that obtain the DNA samples to the software that performs the analysis of these samples. The existing software for methylation analysis does not seem to scale efficiently neither with the size of the dataset nor with the length of the reads to be analyzed. Since it is expected that the sequencers will provide longer and longer reads in the near future, efficient and scalable methylation software should be developed. RESULTS: We present a new software tool, called HPG-Methyl, which efficiently maps bisulfite sequencing reads on DNA, analyzing DNA methylation. The strategy used by this software consists of leveraging the speed of the Burrows-Wheeler Transform to map a large number of DNA fragments (reads) rapidly, as well as the accuracy of the Smith-Waterman algorithm, which is exclusively employed to deal with the most ambiguous and shortest reads. Experimental results on platforms with Intel multicore processors show that HPGMethyl significantly outperforms in both execution time and sensitivity state-of-the-art software such as Bismark, BS-Seeker or BSMAP, particularly for long bisulfite reads. AVAILABILITY: Software in the form of C libraries and functions, together with instructions to compile and execute this software. Available by sftp to anonymous@clariano.uv.es (password "anonymous"). CONTACT: Juan.Orduna@uv.es.},
	keywords = {BS-seq, HPC, methylation, NGS},
	issn = {1367-4811},
	doi = {10.1093/bioinformatics/btv357},
	url = {http://bioinformatics.oxfordjournals.org/content/31/19/3130.long},
	author = {T{\'a}rraga, Joaqu{\'\i}n and P{\'e}rez, Mariano and Ordu{\~n}a, Juan M and Duato, Jos{\'e} and Medina, Ignacio and Joaqu{\'\i}n Dopazo}
}
@article {539,
	title = {Phylemon 2.0: a suite of web-tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing.},
	journal = {Nucleic Acids Res},
	volume = {39},
	year = {2011},
	month = {2011 Jul},
	pages = {W470-4},
	abstract = {<p>Phylemon 2.0 is a new release of the suite of web tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing. It has been designed as a response to the increasing demand of molecular sequence analyses for experts and non-expert users. Phylemon 2.0 has several unique features that differentiates it from other similar web resources: (i) it offers an integrated environment that enables evolutionary analyses, format conversion, file storage and edition of results; (ii) it suggests further analyses, thereby guiding the users through the web server; and (iii) it allows users to design and save phylogenetic pipelines to be used over multiple genes (phylogenomics). Altogether, Phylemon 2.0 integrates a suite of 30 tools covering sequence alignment reconstruction and trimming; tree reconstruction, visualization and manipulation; and evolutionary hypotheses testing.</p>},
	keywords = {Evolution, Molecular, Genomics, Internet, Phylogeny, Sequence Alignment, Software},
	issn = {1362-4962},
	doi = {10.1093/nar/gkr408},
	author = {S{\'a}nchez, Rub{\'e}n and Serra, Fran{\c c}ois and T{\'a}rraga, Joaqu{\'\i}n and Medina, Ignacio and Carbonell, Jos{\'e} and Pulido, Luis and De Maria, Alejandro and Capella-Gut{\'\i}errez, Salvador and Huerta-Cepas, Jaime and Gabald{\'o}n, Toni and Dopazo, Joaquin and Dopazo, Hern{\'a}n}
}
