Confusion in using cactus

[Marh32]

Hi,

I exported axt format files through lastz(human as ref) genome comparison and obtained many pairwise alignments files(Each file is a human reference, e.g Homo_sapiens-Lemur_catta and omo_sapiens-Gorilla_gorilla ) through axtchain and netsytenic, because multiz could not handle closely related species. I want to use cactus instead of multiz to merge the pairwise alignment files into a multi-sequence alignment maf file for subsequent phastcons. But I found that cactus merges maf files by reference to ancestral sequences. I would like to ask which program in cactus can do something similar to multiz and merge my pairwise alignment files (human as ref).

Best regards, Hao Meng

[glennhickey]

Cactus does not provide an interface to specify your own alignments, so if you want a Cactus alignment of this data you will have to start from the assemblies.