Good Morning Max: multiz produces a *multiple* alignment.
An individual chain file is a single alignment between two sequences. multiz is a phylogenetic tree directed multiple alignment. It starts with subsets of the phylo tree with sequences that are already close to each other. As they are combined, new gaps will appear and poorly aligned paired sequences will disappear to produce a better multiple alignment at a higher scale. --Hiram Maximilian Haussler wrote: > Hi genome gurus, > > there is something I've always wondered about in your multiple alignments, > it's how the mafs are produced from the chains. As I've only used pairwise > alignments until now, I was fine with netToAxt and never really understood > what multiz was doing. > > My impression of the whole alignment procedure was that fragments are > aligned using lastz, alignments are combined into chains and nets and > the nets are used to pull out again the best chain-alignments. Then > multiz/autoMZ is reformatting the filtered chains into maf alignments. So I > thought the the chain alignments should correspond to the final maf > alignments. _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
