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