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.
Info
Members (researchers): Ugo Bastolla
Research Groups: Computational biology and Bioinformatics (CBM): from Proteins to Ecosystems
Contact Email: ubastolla@cbm.csic.es
Tool Repository: https://github.com/ugobas/PC_ali
Documentation: https://github.com/ugobas/PC_ali
Publications DOI: doi:10.1093/bioinformatics/btad630
Institution: Centro de Biología Molecular Severo Ochoa (CBM)
Function prediction, Functional genomics, Sequence Alignment, Sequence analysis, Structural bioinformatics
Technical details
Type of application
- Package for compiling the executable program
Software compatibility
- Linux
Hardware requirements
- Any linux computer
Programming language
- C
Type of containerization
- None
Wrapper type
- None
Input file formats
- fasta
- pdb
Output file formats
- fasta
- Other
- pdb