Hi,
I am new to bioinformatics and would like to know if there is any recommended software to compare for example:
Let's say I have multiple files (fasta for example) from complete genomes and want to compare their similarity % or/and if they share the same origin.
Something like different bat coronavirus and human genomes.
I tried to make my own python script but it is a hassle and very time consuming.
Thanks
FastANI rapidly compares fasta sequences and will output global identity. It is meant only for relatively similar genomes, and will not create any output if identity is below 75-80%.
This sounds useful as I used pairwise using blastn and achieved 96% and 85% per ident for the sequences that were supposed to be similar when compared to the main sequence. The other sequences had bad e-values and similarity lower than 67%.
MAFFT is another tool that could also employ
https://mafft.cbrc.jp/alignment/software/
that being said the task of comparing bat coronaviruses is incomparably simpler than comparing human genomes.
radically different methodologies would be needed in the latter case.
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Is there any way to do this using R?