maximum likelihood ancestral amino-acid sequence reconstruction
FastML is a bioinformatics tool for the reconstruction of ancestral
sequences based on the phylogenetic relations between homologous
sequences. FastML runs several algorithms that reconstruct the ancestral
sequences with emphasis on an accurate reconstruction of both indels and
characters. For character reconstruction the previously described FastML
algorithms are used to efficiently infer the most likely ancestral
sequences for each internal node of the tree. Both joint and the
marginal reconstructions are provided. For indels reconstruction the
sequences are first coded according to the indel events detected within
the multiple sequence alignment (MSA) and then a state-of-the-art
likelihood model is used to reconstruct ancestral indels states. The
results are the most probable sequences, together with posterior
probabilities for each character and indel at each sequence position for
each internal node of the tree. FastML is generic and is applicable for
any type of molecular sequences (nucleotide, protein, or codon
sequences).
