PC_ali
PC_ali performs hybrid multiple structure and sequence alignments based on the structure+sequence similarity score PC_sim. Besides the MSA, it outputs pairwise similarity scores and divergence scores and neighbor-joining phylogenetic tree obtained with the hybrid evolutionary divergence measure based on PC_sim, and it outputs a pdb file with multiply superimposed structures. Optionally, it computes violations of the molecular clock for each pair of proteins.
Basic Information
| Repository | https://github.com/ugobas/PC_ali |
| Documentation | https://github.com/ugobas/PC_ali |
| Seminar | Ugo Bastolla presents the tools TNM, PC_ali & SSCPE |
| Main publication (DOI) | 10.1093/bioinformatics/btad630 view |
| Contact email | ubastolla@cbm.csic.es |
| Authors/Maintainers | Ugo Bastolla |
| Type of application | Package for compiling the executable program |
| Programming languages | C |
| Keywords | Computational Methods, Functional genomics, Function prediction, Structural bioinformatics, Sequence analysis, Sequence Alignment |
Technical details
| Input file formats | fasta, pdb |
| Output file formats | fasta, pdb, Other |
| Software compatibility | Linux |
| Hardware requirements | Any linux computer |
| Type of containerization | None |
| Wrapper type | None |
| Compatible tools | |
| Funding resource | National competitive funding |
| Funding support | No funding |
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| Citations (last 12 months) | <100 (~2 as of 15/10/2026) |
| Citations (since first release) | <100 (7 as of 15/10/2026) |
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