Hello Munir,
One of our developers suggests running blastz to get pairwise local alignments, and then some tool(*) to choose a single-coverage subset of the alignments, e.g. lavToPsl | axtChain -psl | chainNet | netToAxt | axtToMaf and feed the resulting pairwise maf to multiz. Please also see this wiki document on the topic: http://genomewiki.cse.ucsc.edu/index.php/Whole_genome_alignment_howto I hope this information is helpful to you. Please don't hesitate to contact us again if you require further assistance. Kayla Smith UCSC Genome Bioinformatics Group ----- Original Message ----- From: "Munirul Islam" <[email protected]> To: [email protected] Sent: Wednesday, March 11, 2009 7:59:38 AM GMT -08:00 US/Canada Pacific Subject: [Genome] on multiz tba tool Hi: I am new to multiz-tba tool available at http://www.bx.psu.edu/miller_lab/. I could install it. Now I would like to use the tool to align a fasta file containing sequences from multiple species. Can someone suggest how to do it? I really appreciate your time. Munir -- ============================= Munirul Islam Graduate Research Assistant Center for Molecular Medicine and Genetics Wayne State University Detroit,MI-48201,USA PhD Candidate Department of Computer Science Wayne State University Detroit,MI-48202,USA email: [email protected] _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
