Hey community :)
I want to first conduct an alignment on my bacterial genomes (these vary in size) for which I was thinking of using something like Mauve or Clustalw to conduct multiple genome alignments to measure their evolutionary relationships. After the alignment I wanted to carry out the annotation of various gene clusters over the alignment.
1) Which software/algorithm would you recommend to run the alignment (bacterial genomes), hopefully can be run from the bash command line :) I was thinking of either Mauve or ClustalW.
2) Which software or program would be recommended to carry out the annotations of the gene clusters (I have seperate .gbk files for each gene cluster)? I was considering possibly Geneious but this has to be purchased or used with a trial version.
Thank you and best regards!
For the first part, I think it might be easier if you find the marker genes in those reference genomes and align them to build a gene tree rather than a species tree using Muscle or MAFFT,..:
Gene tree:
https://www.nature.com/articles/nbt.3886
Species tree:
https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-016-3407-6
Thanks Fatima! i will check this out for sure :)