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Can chromap deal with haplotypes

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Hi, I want compared the difference between two haplotypes. Can chromap directly alignment two haplotypes? If I want to get alignmet files of two haplotypes precisely. How to get it?

Hi, Is there a recommend ways to filter cactus result. I used hal2maf to export the maf file below. But I think it is too crush to analysis. Species in...

Hi, I used the super-matrix and coalescent methods to construct a species tree by 4000 single copy orthologs. When I counted ABBA analysis, I found that ABBA (628,561) pattern more...

Can Nexus format tree replace NHX format tree?

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Thanks a lot for convenient tools. I have question about input gene tree. Can Nexus format tree replace NHX format tree? Or you have recommend methods transfrom Nexus format tree...