Hello, help me.
I need to work with the useful OrthoANI (OAT command line) which measures the global similarity between genomes. I'm working on 145 genomes so per command line it will be good but standard software.
I never used orthoANI but the usage is pretty simple, it is an all vs all. What did you try so far?
all vs all
I haven't found the solution yet. by graphical interface you have the right for 10 genomes but for 145 impossible that's why I chose command line, but I don't know how to do it?
for f1 in /path/to/genomes_fasta/*
for f2 in /path/to/genomes_fasta/*
java –jar ./OAT_cmd.jar -blastplus_dir /path/to/NCBI/blast_version/bin/ –fasta1 "$f1"-name –fasta2 "$f2"
I never used orthoANI before so I would try this with few genomes e.g. 5 to see if it works. Alternatively you could try pyani
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