How to get multiple alignment with Multiz?

[jintingguan]

Hello,

I have gotten local alignments by using Blastz, then how to get a multiple alignment with Multiz and what the command is.

For example , I use Blastz to align human and mouse and get HM.maf.
Then I use Blastz again to align human and rat and get HR.maf.

How can I use these results HM.maf and HR.maf to get a multiple alignment with Multiz?

Thank you in advance for your help.

Regards,
Guan

 

[Hiram Clawson]

Good Morning Guan:

Use the documentation in the Multiz package to operate multiz.
Download multiz from here:
http://www.bx.psu.edu/miller_lab/

The autoMZ controlling program in the multiz package is also
called 'roast'

Examples of how UCSC uses autoMZ can be found in our make doc.
For example, anoCar2.
http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=blob;f=src/hg/makeDb/doc/anoCar2.txt

--Hiram