Hello Mauve users,
I have aligned ~40 complete genomes from isolates of the same bacteria species
using the progressiveMauve command-line application and the unannotated FASTA
genome sequences. These genomes are closely related, but often differ in their
organization owing to a number of rearrangement (inversions) and IS-element
insertions. I'm interested to further analyze the .backbone file to reconstruct
possible phylogenetic relationships between these genomes based on genome
order/organization and content, which has lead me to the following questions:
1. What parameters most determine the stringency of defining homology
between conserved segments (and what are the defaults)? Meaning, what dictates
the cut-off between defining segments from two genomes as being the 'same'
(same row of .backbone) or 'different' (different rows)?
2. Have others tried to ask similar questions with the .backbone output?
I know there are tools for inferring rearrangement histories using
BADGER/GRAPPA-like permutation matrices, including MLGO which now allows blocks
shared among only a subset of genomes. And so it seems proper tuning of the
parameters for segment homology definition could provide improved resolution to
such phlyogenies.
Thanks for any thoughts/feedback you might have.
====================
Michael R. Weigand, PhD
Bioinformatician | IHRC
NCIRD/DBD/MVPDB
Centers for Disease Control and Prevention
mweig...@cdc.gov<mailto:mweig...@cdc.gov>
404.639.2473
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