MUGSY not able to perform alignment ?

Question

[sunnykevin97]

Here, I tried to align Chr24 of much closer genomes of elephants it is able to generate a MAF. But, I was expecting an alignment that is gene by gene, and only including the coding regions. CMD

./mugsy --directory /home/Downloads/mugsy/mugsy_x86-64-v1r2/ --prefix mychr  /home/Documents/chr24/chr24.fa /home/Documents/chr24/testReadGroups.bam_CHr24_GATK1.vcf.fa /home/Documents/chr24/test1_Ddedup_2_ReadGroups_chr24.bam_GATK.vcf.fa

The output looks like this, not able to interpret the result.

##maf version=1 scoring=mugsy
a score=1512771 label=1 mult=3
s chr24.LoxArf        5053396 1487445 + 27123610 TGGTGTGTTGAAGTCTCCTACTATAATTGTGGAGGTATCTATCTCACTTTTCAATTCTGTTAAAATTTGATTTATGTATCTTGCAGCCCTGTCATTGGGTGCATAAATATTTAA
TATGGTTATGTCTTCCTGGTCAATTGTCCCTTTTATCATTATATAGTGTCCTTCTTTATCCTTTGTGGTGGATTTAAGTCTAAAGTCTATTTTGTCAGAAATTAATATTGCTACTCCTCTTCTTTTTTGCTTATTGTTTGCTTGATATACTTTTTTCCATCCTTT
GAGTTTTAGTTTGTTTGTGTCTCTAAGTCTAAGGTGTGTCTCTTGTAGGCAGCATATAGATGGATCGTGTTTCTTTATCCAGTCTGTGACTCTCTGTCTCTTTATTGGTGCATTTAGTCCATTTACATTCAGGGTAATTATAGATAAATAAGTTTTTAGTGCTGTCATTGTGATGCCTTTTTATGTGTGTTGTTGACAATTTCATTTTTCCACATA

Mugsy, can handle sequences from closely related genomes. Is their any other alignment tools which generates alignment in MAF (Multiple alignment format). And which are able to align much more distant genomes ?

Thanks!

[WouterDeCoster]

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[h.mon]

From the manual:

Mugsy is a multiple whole genome aligner.

Mugsy aligns whole chromosomes / genomes, it won't output a gene by gene alignment. If you want a gene by gene alignment, you should look at orthology software - but you have to predict the genes first.