BLASTP Dependency Integrated

BLASTP dependency included and tested for correct execution in xml mode
Kalign dependency integrated

Tests for kalign running and execution utility function moved to test
base class
Integrated trimal dependency

Bundled trimal dependency is now tested and included
FastTree dependency integrated

FastTree is not tested and built into the repo
Merge bundled_dependencies feature into develop

Incorporate the bundled dependencies into the main develop branch