Mulan :: MUltiple sequence Local AligNment and conservation visualization tool

Mulan performs full local alignment of multiple nucleotide sequences. It can be applied to the analysis of distant (such as humans and fish, for example) or closely related (such as humans and primates or mice and rats) species. Mulan performs both tba-based alignments for "finished"-quality sequences and refine-based alignments for "draft"-quality sequences (that are represented as a set of separated contigs). Some of the options available for Mulan users include: · Dynamic graphical visualization of conservation profiles with a number of options for data presentation. · Pairwise dot-plots displaying alignment blocks and overview of evolutionarily rearrangements. · Dynamic batch detection of ECRs (Evolutionarily Conserved Regions) by varying ECR parameters for each of the pairwise alignments. · Static refine and dynamic tba FASTA alignment files. · Phylogenetic trees. · Portal to the multiTF tool for detection of cross-species TFBS. (Available for "finished" Mulan alignments.) · Possibility to dynamically modify gene annotation. · Download of input sequences in the original format and with repetitive elements masked by .N. symbols as well as an annotation of types of repetitive elements.       Please refer to the Mulan instructions for the description of the tool usage.       Mulan was developed by Ivan Ovcharenko in collaboration with Gabriela G. Loots, Lisa Stubbs, Belinda M. Giardine, Minmei Hou, Jian Ma, Ross C. Hardison, and Webb Miller.       If you find this tool useful in your research please cite it as (I. Ovcharenko, G.G. Loots, B.M. Giardine, M. Hou, J. Ma, R.C. Hardison, L. Stubbs, and W. Miller, Mulan: Multiple-sequence local alignment and visualization for studying function and evolution, Genome Research, 15, 184-194 (2005) [PDF]).