PyMod 3 - sequence similarity searches, multiple sequence/structure alignments, and homology modeling within PyMOL.
Files for PyMod 3. Current version: PyMod 3.0.2 (last update 17/8/2020). From here, you can download a ZIP file with the PyMod 3 plugin (pymod3.zip), which can be installed as a regular plugin on PyMOL (version >= 2.3.4 for incentive builds; version >= 2.3.0 for open source builds) and the User's Guide of the plugin (pymod_users_guide.pdf). You do not need to download the installer_bundle.zip files, they will be automatically downloaded when you use the external tools installation dialog in the plugin.
Legacy PyMod 2.0 files. PyMod 2.0 was compatible with PyMOL 0.99 and 1.X. From here you can download PyMod 2.0 Installer Bundle .zip files. Version 2.0.8, last updated: 3/11/2017.