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wang-q / multiz

A strip-down version of multiz-tba
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Multiz multiple species #1

Open madzafv opened 6 years ago

madzafv commented 6 years ago

Hi, does the version of Multiz in this repository works for aligning more than two species to a reference? Thanks

wang-q commented 6 years ago

Hi madzayasodara,

multiz from this repo does the same function as the original one. I just removed some unnecessary codes and made it supporting gzipped maf files.

For multiple genome alignments, you should:

  1. produce multiple pairwise alignments with lastz against the reference genome;
  2. convert axt files to maf;
  3. join pairwise maf files with multiz.
multiz t/Q_rubravsQ_aliena/mafSynNet/NC_020152.synNet.maf.gz \
      t/Q_rubravsQ_aquifolioides/mafSynNet/NC_020152.synNet.maf.gz \
      1 out1 out2 > step1.NC_020152.maf
multiz step1.chr1.maf t/Q_rubravsQ_baronii/mafSynNet/NC_020152.synNet.maf.gz \
      1 out1 out2 > step2.NC_020152.maf
AlisaGU commented 3 years ago

@wang-q, If I get it, multiz just join two maf file. If I want to get 4 species including target genome alignment, I need to run multiz 2 times like that:

multiz A_B.maf A_C.maf 1 out1 out2 >A_B_C.maf
multiz A_B_C.maf A_D.maf >A_B_C_D.maf

Is it right?

wang-q commented 3 years ago

Yes, you can do this.