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.
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
Source code for all programs other than the gibbs samplers (uploaded on 5/24/23):
Funding:
National Institutes of Health, National Institute of General Medical Sciences grants R01GM078541 & R01GM125878.
National Institutes of Health, National Library of Medicine grant R01LM06747.