ModelGenerator and MultiPhyl Online

MultiPhyl is the first high-throughput implementation of a distributed phylogenetics platform that is capable of using the idle computational resources of many heteogeneous non-dedicated machines to form a phylogenetics supercomputer. MultiPhyl allows a user to upload hundreds or thousands of amino acid or nucleotide alignments simultaneously and perform computationally intensive tasks such as model selection, tree searching, and bootstrapping of each of the alignments. The program implements a set of 88 amino acid models and 56 nucleotide ML models and a variety of statistical methods for choosing between alternative models using code from ModelGenerator.

Web Submission Form

Please feel free to try ModelGenerator or MultiPhyl by uploading your datsets using the form below. Please note that jobs received via this service will receive a lower priority on our system than simultaneous analyses being carried out by our lab and therefore may take longer to execute. Results are emailed back to the user when the analysis is finished. User documentation for MultiPhyl Online is available from here.

Note: If you wish to analyse more than one alignment - please upload a single zip file containing all your alignments. All alignments must be in either Fasta or Phylip format and taxa names should not contain any spaces, commas, semi-colons, or brackets.

Alignment File

Analysis Options
Model Selection	YES
Model Selection Measure
Number Gamma Categories
Perform Tree Search
Tree Search Algorithm
Initial Tree
SPR Level
Perform Bootstrapping
Number of replicates
User Details
Name
Institution
Email Address

We currently have MultiPhyl deployed across approximately 400 desktop machines at NUI Maynooth - if you are interested in pooling your group of desktop machines with our cluster then please contact us.

MultiPhyl Online Documentation

A user manual for MultiPhyl Online is available to view here. It describes the acceptable data formats, analysis options, output files, and the algorithms used.

Citation

If you use MultiPhyl please cite:
Thomas M Keane, Thomas J Naughton, James O McInerney (2007) MultiPhyl: A high-throughput phylogenomics webserver using distributed computing, Nucleic Acids Research, 35:W33-W37. link

If you use ModelGenerator please cite:
Thomas M Keane, Christopher J Creevey , Melissa M Pentony, Thomas J Naughton and James O McInerney (2006) Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified, BMC Evolutionary Biology, 6:29 link

A complete description of MultiPhyl is available in Chapter 4 of this PhD Thesis.