GLOOME Server - Gain Loss Mapping Engine
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Research Site | Pupko Group

Type your phyletic pattern MSA (FASTA format only)
Have genomic sequences?
Use M1CR0B1AL1Z3R web server to extract a phyletic pattern MSA!


OR
Upload your MSA file (FASTA format only)    

Type your phylogenetic tree (Optional) (Newick format only)

Optional and recommended input: the assumed tree topology (with or without branch lengths); Note: tree format must not include names for inner nodes

OR
Upload phylogenetic tree file (Newick format only)     

(+) Evolutionary model
The probabilistic model describing the gain and loss dynamics

gain & loss rates
  1. "Fixed gain/loss ratio": gain and loss probabilities may be different but the gain/loss ratio is identical across all sites.
  2. "Equal gain and loss": the probability of a gain event is assumed to be equal to that of a loss event.
  3. "Variable gain/loss ratio (mixture)": gain/loss ratio varies among sites.


Rate distribution (show more rate distribution)
  1. "Equal": assume that a single evolutionary rate characterizes all sites.
  2. "Gamma": among site rate variation, assuming that the rate is gamma distributed

Allow root freq to differ from stationary ones
In stationary processes the character frequencies are equal across the entire tree. Use this option to analyze the data using non-stationary models.


Loss only model (gain rate ~ 0)

(+) Correction for un-observable data

Minimum number of ones
If zero is selected the model allows sites with only zeros to appear (do not account for un-observable data). Select more than one if singletons are also un-observable.


Minimum number of zeros
If zero is selected the model allows sites with only ones to appear. Select one if variable sites are required (e.g., for indel data).

(+) Results
(+) Stochastic mapping
The stochastic mapping approach infers for each branch and each site the probability and expected number of both gain and loss events. This information is provided both textually (with additional files for sum over branches or over sites) and visually (color-coded phyletic pattern)

Expected number of events per site

Expected number of events per branch

Probability and expectation of events per site per branch

(+) Parsimony
Under the parsimonious assumptions for each branch and each site the number of both gain and loss events is computed

Parsimony cost of gain
The relative costs of gain and loss events can be determined by the user. E.g., select: cost of gain=2, if the gain events should twice as costly as loss events

Parsimony count of events per site

Parsimony count of events per branch

Parsimony count of events per site per branch

(+) Additional features
Likelihood based computations.

Rate per site
The posterior estimation of the relative rate of each site


Calculate gain and loss per site
Separate estimation of the gain and loss rates for each site (mixture model only)


Likelihood per site
The log-likelihood for each site


Estimated tree
The tree and its associated branch lengths estimated from the phyletic pattern. A Java applet is available for tree visualization and manipulation.


Log verbosity level

(+) Advanced
Estimate all model parameters using likelihood Yes   No
Likelihood estimation of parameters can be avoided by setting their values based on character counts directly from the phyletic pattern.

Estimate branch lengths using likelihood Yes   No
Likelihood estimation of branch lengths can be avoided and the input branch lengths or initial estimation is used.

Estimate parameters with multiple random starting points Yes   No
Choose this option to avoid local maxima in maximum likelihood estimation of parameters

Optimization level
Running times can be modified by changing the optimization level.

Number of rate categories
The continues gamma distribution is approximated with discrete number of categories. For number of categories > 4 the computation time may be long.

Compute ancestral reconstuction of states

(+) Simulate phyletic patterns

Simulate phyletic patterns Yes   No
Choose this option to perform phyletic patterns simulation with stochastic mapping and maximum parsimony detection of events for simulated data.
The phyletic patterns are simulated along the input tree with number of organisms corresponding the input MSA (input phyletic pattern)

Simulated evolutionary scenario

loss/gain ratio

Number of site to simulate

Number of replication for each simulation scheme

Send a link to the results by e-mail (optional)