PhaSePred
Copyright (c) 2026 Tingting Li Lab, Department of Biochemistry and Molecular
Biology, School of Basic Medical Sciences, Peking University.

This product is licensed under the MIT License; see LICENSE.

Third-party components
======================

Vendored in this repository
---------------------------

PLAAC   MIT (Whitehead Institute, BBRI, UMass)
        License text: tools/PLAAC/plaac-master/LICENSE.TXT
        Usage and provenance: tools/PLAAC/README.md

PScore  CC-BY-4.0 (Vernon et al., eLife 2018)
        Attribution is required by the licence. Source and terms:
        tools/PScore/README.md. The PScore DBS data is not redistributed;
        tools/PScore/install.sh fetches it.

SEG     NCBI public-domain convention
        tools/SEG/README.md

DeepPhase lookup table   MIT
        Redistributed with the package. Licence text and attribution:
        src/phasepred/data/deepphase/LICENSE and
        src/phasepred/data/deepphase/NOTICE

Installed by the user, not redistributed here
---------------------------------------------

ESpritz           Tosatto academic licence; the archive must be supplied by the
                  user. tools/ESpritz/README.md
DeepCoil          tools/DeepCoil/README.md
PhosphoSitePlus   CC-BY-NC-SA-3.0; redistribution is not permitted, so
                  tools/PhosphoSitePlus/install.sh fetches it after
                  registration. tools/PhosphoSitePlus/README.md
LocalCIDER        GPL-2.0, a separate PyPI dependency. It supplies both the
                  Hydropathy and FCR feature columns; there is currently no
                  equivalent non-GPL implementation and no configuration
                  switch. tools/LocalCIDER/README.md

Every tool directory also carries a machine-readable manifest.toml whose
`license` and `redistributable` fields are the authoritative statement for
that component; `phasepred check-tools` prints both.

Other attributions
==================

The catGRANULE scoring implementation derives from Bolognesi et al. 2016
(Cell Reports 16:222-231) and is provided by the separate `catgranule`
package under the MIT License.

PhaSePred reproduces the models and evaluation of Chen et al. 2022,
"Screening membraneless organelle participants with machine-learning models
that integrate multimodal features", PNAS 119(24) e2115369119.
https://doi.org/10.1073/pnas.2115369119
