Software

SPARC: Structural Properties Associated with Residue Constraints

DARC: Deep Analysis of Residue Constraints

STARC: Statistical Tool for Analysis of Residue Couplings

SIPRIS: Structurally Interacting Pattern Residues’ Inferred Significance 

BPPS: Bayesian Partitioning with Pattern Selection

MAPGAPS: Multiply-Aligned Profiles for Global Alignment of Protein Sequences

The website includes CDD2MGS for creating MAPGAPS input files from NCBI CDD files,  AddPhylum for phylum and kingdom taxonomic labeling of protein sequences, and PurgeMSA for eliminating fragments and redundant sequences.

GISMOGibbs Sampler for Multi-alignment Optimization

eCOMPASS: evaluative Comparison of Multiple Protein Alignments by Statistical Score

LAPIS: Lots of Accurately-aligned Proteins Initiated from Scratch

Gibbs motif/site sampler  

A program for identifying conserved segments in protein sequences. It is particularly useful for identifying internal repeats.  Gibbs sampling is named after the physicist Josiah Willard Gibbs, in reference to an analogy between the sampling algorithm and statistical physics.

Auxiliary programs: CDD2MGS, AddPhylum, PurgeMSA, ConvertMSA, VSI2PML, TweakCMA, TweakPDB, and GetPDB

Latest versions of source code for all programs other than the gibbs samplers

Tutorial on the use of these programs

Funding:

National Institutes of Health, National Institute of General Medical Sciences grants R01GM078541 & R01GM125878.

National Institutes of Health, National Library of Medicine grant R01LM06747.