https://github.com/seqan/lambda/wiki/LAMBDA-%E2%86%92-lambda2-guide
The CLI has significant changes:
Lambda1 had two executables: lambda and lambda_indexer
Lambda2 has a single executable: lambda2
lambda2 has different sub-commands
The on disk format has changes:
Lambda now stores it's index files in a separate folder instead of cluttering the directory where your original .fasta file was. These folders have a .lambda extension, but are regular folders that just contain the different data files needed.
There doesn't appear to be an auto-upgrader or shim script provided for lambda v1 users.
However, there are no references from other Debian packages to lambda-align's binaries, so upgrading to v2 without changing the package name won't break any packages, but it will break user scripts.
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Direktorius, VšĮ "Darbo eigos", Vilnius, Lithuania