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AlignmentProcessor1.4

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@icwells icwells released this 22 May 20:19
· 13 commits to master since this release

Fixed bug causing Exec formatting error when running CodeML on servers.
Fixed bug causing only first species in low quality alignment to be filtered out.
Writes CodeML stdout to logs in tmp folders. Stderr is printed to the screen.
Allows users to specify their own phlyogenic tree.