Any command starting with
blastall is the old version of BLAST.
We strongly encourage users of the legacy C toolkit applications (e.g, blastall, blastpgp, etc.) to use the new BLAST+ applications. The BLAST+ applications have a number of new features and enhancements such as database masking, more flexibility in tabular formatting, indexed megaBLAST, and the ability to save results and reformat searches. Many of these are described in http://www.ncbi.nlm.nih.gov/pubmed/20003500 and http://www.ncbi.nlm.nih.gov/pubmed/18567917. More importantly, the BLAST+ applications use a completely redesigned framework that fixes a number of issues in the legacy applications ...
You can convert old BLAST scripts using
blastall to the new BLAST+ syntax with the NCBI tool:
legacy_blast.pl [YOUR COMMAND] --print_only
If you really want to stick with
blastall, the NCBI periodically fixes bugs in the old version, but won't improve it or add any new features: Old Blast FTP