Problems Running The Ncbi-Blast Tools

Question

[Naren]

I want to find core genome of around 30 bacterial genomes. For that I have Installed NCBI-BLAST package from NCBI FTP site using ncbi-blast-2.2.27+-win64.exe I have set environment variable PATH="C:\Program Files\NCBI\blast-2.2.27+\bin". Still it is not running the commands formatdb -i 1.txt -p F -o F and blastall -p tblastx -d 1.txt -i 2.txt -o 1vs2.txt -m 8 -a 3

What else do I need to do to accomplish the task? Thanks in advance.

Answer 1

[Istvan Albert]

You have installed blast+ make sure to use the blast+ commands instead of the blast commands.

makeblastdb instead for formatdb etc

If you find this ridiculous you are not alone.

[Naren]

Hello, @albert: is there any manual to see all those commands like -o, -i , blastall which are used in Blast+,?

Answer 2

[Lee Katz]

Tons of people are using OrthoMCL for this task. I also had the benefit of learning about Dave Ussery's CMG-Biotools which can give you the core genome, plus a publication-ready figure.