[交流] 请问各位大牛们知道全基因组three-way alignments 怎么操作的吗

RT，请问各位大牛们知道全基因组three-way (species) whole-genome sequence alignments in MAF format (UCSC)怎么操作的吗 To perform an exhaustive, genome-wide screening for phyloge- netically informative retroposon insertions in placentals and to test the three viable phylogenetic hypotheses of the basal origin of placentals, we derived two different three-way (species) whole-genome sequence alignments in MAF format (UCSC): (1) armadillo–elephant–human (3050 gigabases) and (2) elephant– human–armadillo (2730 gigabases), the decisive difference between the two alignments being the full retroposon represen- tation of the leading species that was used as the profile for the remaining species. The three-way alignments were prepared using pairwise (armadillo–elephant and armadillo–human for the first three-way alignment and elephant–human and armadillo–elephant for the second three-way alignment) BLASTZ alignments (Chiaromonte et al. 2002; Kent et al. 2003; Schwartz et al. 2003) and the standard matrix used in the UCSC browser. The alignments were fed into axtChain with the parameters chainMinScore = 3000  chain- LinearGap = medium, which organizes all alignments by chro- mosome (or scaffold) and creates a kd-tree from the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find themaximally scoring chains of these blocks. Finally, MULTIZ (Blanchette et al. 2004) was used to generate the two three-way alignments referencing elephant and armadillo. We used the first alignment to search for elements supporting the Atlantogenata [(armadillo + elephant)  human] and Exa- froplacentalia [(armadillo + human)  elephant] hypotheses, and the second one to test the Epitheria [(elephant + human)  armadillo] hypothesis. 这是原文，我对生物信息一点基础都没有，无奈老板非要我做，求助啊

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