Prof. Tal Pupko

Tal Pupko - Software Tal Pupko - Software:

Computer programs and web servers:

Phylogeny and functional genomics:
1. FASTML web server - for ancestral sequence reconstruction (including both the dynamic programming- and the branch-and-bound algorithms and the C++ source code)
2. RATE4SITE (version 2.01) a program for computing the evolutionary rate at each amino acid
3. The COMBINE program and supplementary information for the "Combining Multiple Sequences" paper
4. Consurf - a web server for the identification of functional regions in proteins with known 3D structure
5. Conseq - a web server for The identification of functionally and structurally important residues in protein sequences
6. Selecton - a web server for the identification of site-specific selection (positive and purifying selection)
7. SEMPHY - a program for maximum-likelihood based phylogenetic tree reconstruction
8. Source code for computing the likelihood of a tree and site-specific rate using a gamma mixture model
9. GUIDANCE - a web server for assigning a confidence score for each residue, column, and sequence in an alignment
10. GLOOME - a web server for analyzing 0/1 matrrices in an evolutionary context. GLOOME can map gain and loss events onto a phylogenetic tree using a stochastic mapping approach
11. RASER - a web server implemeting a likelihood based method for testing and detecting site-specific evolutionary rate shifts
12. TraitRateProp - a web server for detecting trait-dependent evolutionary rate shifts in sequence sites
13. CoPAP - Co-evolution of Presence-Absence Patterns
14. SpartaABC - a web server to simulate sequences based on indel parameters inferred using an approximate Bayesian computation algorithm
16. ModelTeller - A machine learning tool for phylogenetic model selection
17. SINCOPA - a web server for detecting selective sweeps in bacteria
18. EvoRator - a web server for prediction of residue-level evolutionary rates from protein structures

1. M1CR0B1AL1Z3R - a web server for analyzing bacterial genomics data
2. Effectidor - a web server for predicting type III effectors

1. Pepitope - a web server for epitope mapping using affinity-selected peptides
2. Epitopia - a web server for detecting immunogenic regions in protein structures or sequences
3. ASAP - a web server for Ig-Seq Analysis Pipeline
4. PASA - a web server for Proteomics Analysis of Serum Antibodies