represent gene loss and duplication. Web applications Finally, there are several web-server based applications that allow investigators to use maximum likelihood methods for ancestral reconstruction of different character types without having to install any software. For example, Ancestors is web-server for ancestral genome reconstruction by the identification and arrangement of syntenic regions. FastML is a web-server for probabilistic reconstruction of ancestral sequences by maximum likelihood that uses a gap character model for reconstructing indel variation. MLGO is a web-server for maximum likelihood gene order analysis. Future directions The development and application of computational algorithms for ancestral reconstruction continues to be an active area of research across disciplines. For example, the reconstruction of sequence insertions and deletions (indels) has lagged behind the more straightforward application of substitution models. Bouchard-Côté and Jordan recently described a new model (the Poisson Indel Process) which represents an important advance on the archetypal Thorne-Kishino-Felsenstein model of indel evolution. In addition, the field is being driven forward by rapid advances in the area of next-generation sequencing technology, where sequences are generated from millions of nucleic acid templates by extensive parallelization of sequencing reactions in a custom apparatus. These advances have made it possible to generate a "deep" snapshot of the genetic composition of a rapidly evolving population, such as RNA viruses or tumour cells, in a relatively short amount of time. At the same time, the massive amount of data and platform-specific sequencing error profiles has created new bioinformatic challenges for processing these data for ancestral sequence reconstruction. See also Evolutionary biology Origin of life Enzyme promiscuity Ancestral sequence reconstruction References Evolutionary biology