FastML

FastML

FastML is a tool for reconstructing ancestral sequences. FastML implements various novel features that differentiate it from existing tools: (i) FastML uses an indel-coding method, in which each gap, possibly spanning multiples sites, is coded as binary data. FastML then reconstructs ancestral indel states assuming a continuous time Markov process. FastML provides the most likely ancestral sequences, integrating both indels and characters; (ii) FastML accounts for uncertainty in ancestral states: it provides not only the posterior probabilities for each character and indel at each sequence position, but also a sample of ancestral sequences from this posterior distribution, and a list of the k-most likely ancestral sequences; (iii) FastML implements a large array of evolutionary models, which makes it generic and applicable for nucleotide, protein and codon sequences; and (iv) a graphical representation of the results is provided, including, for example, a graphical logo of the inferred ancestral sequences. An alternative public server is available here: [url=http://fastml.tau.ac.il/]http://fastml.tau.ac.il/[/url]

Input files: FastML accepts as input Protein or DNA matrices in aligned fasta format.

Output files: Ouput files are returned as a .zip archive that can be downloaded and unpacked locally. This includes a folder of input for JalView, and a folder for Indels reconstruction.

The table below provides a test input file for FastML:

Input File Names Sample File from a Test
alignment file fastml_infile.txt
   

If you use FastML here, please cite:

If there is a tool or a feature you need, please let us know.

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