This is the walkstrough how to identifiy genome-wide synteny markers based on LASTZ alignment. I used it to identify the syntenic markers for O. saiva (rice) and O. brachyantha, they diverged each other 15 million years ago.
Step1：Mask the repeat sequences for both genomes and chromosomes.
RepeatMasker -pa 40 -nolow -norna -gff -xmall -lib custom.TE.lib_for_rice.fa AAChr1.txt RepeatMasker -pa 40 -nolow -norna -gff -xmall -lib custom.TE.lib_for_FF.fa FFChr1.txt
Step2: Alignment using LASTZ and Chain/Net
lastz AAChr1.txt FFChr1.txt K=2200 L=6000 Y=3400 E=30 H=0 O=400 T=1 --format=axt --out=chr01.axt axtChain -linearGap=medium chr01.axt AAChr1.txt FFChr1.txt chr01.axt.chain chainPreNet chr01.axt.chain AAChr1.txt.sizes FFChr1.txt.sizes chr01.chain.filter chainNet chr01.chain.filter -minSpace=1 AAChr1.txt.sizes FFChr1.txt.sizes chr1.chain.filter.tnet chr1.chain.filter.qnet netSyntenic chr1.chain.filter.tnet chr1.chain.filter.tnet.synnet netToAxt chr1.chain.filter.tnet.synnet chr1.chain.filter.tnet.synnet chr01.chain.filter AAChr1.txt FFChr1.txt chr1.chain.filter.tnet.synnet.axt axtSort chr1.chain.filter.tnet.synnet.axt chr1.chain.filter.tnet.synnet.Sort.axt axtToMaf chr1.chain.filter.tnet.synnet.axt AAChr1.txt.sizes FFChr1.txt.sizes -tPrefix=target. -qPrefix=query. chr1.chain.filter.tnet.synnet.axt.maf
Step 3: Get syntenic markers
perl Maf2rawsynteny.pl chr1.chain.filter.tnet.synnet.axt.maf target.AAChr1 query.FFChr1 perl Get_synteny.pl -i chr1.chain.filter.tnet.synnet.axt.maf -n 0 -m 3 -t target.AAChr1 -q query.FFChr1 -o syn.final.out