Questions tagged [mauve]

Questions regarding the Multiple Genome Alignment software Mauve developed by the Darling lab.

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5
votes
0answers
74 views

What does it mean if aligned genomes are not of the same length?

I am aligning 4 genomes of Psuedomonas chlororaphis using progressive mauve software. Command used: ...
0
votes
1answer
158 views

Find a map/correspondence between two versions of a genome

I am working with two versions of the C. elegans genome. I am finding interesting regions (specifically, tRNA genes) in version 1 and then I would like to know if version 2 also has a tRNA gene in ...
7
votes
3answers
2k views

visualisation of genome alignment

I was asked to check the synteny of some genes in two genome assemblies of the same species (PacBio & Illumina). I was given two scaffolds couples (so 4 scaffolds total) in the Illumina genome and ...
2
votes
1answer
403 views

Can I export the SNPs between whole genome alignments using the command line?

I am using Mauve to align two whole genomes. I use the following command to get the alignment in xmfa format: ...