Ancestors 1.0: a web server for ancestral sequence reconstruction.
CONCLUSIONS
The computational inference of ancestral genomes consists of five difficult steps: identifying syntenic regions, inferring ancestral arrangement of syntenic regions, aligning multiple sequences, reconstructing the insertion and deletion history and finally inferring substitutions. Each of these steps have received lot of attention in the past years. However, there currently exists no framework that integrates all of the different steps in an easy workflow. Here, we introduce Ancestors 1.0, a web server allowing one to easily and quickly perform the last three steps of the ancestral genome reconstruction procedure. It implements several alignment algorithms, an indel maximum likelihood solver and a context-dependent maximum likelihood substitution inference algorithm. The results presented by the server include the posterior probabilities for the last two steps of the ancestral genome reconstruction and the expected error rate of each ancestral base prediction.


BACKGROUND
The Ancestors 1.0 is available at http://ancestors.bioinfo.uqam.ca/ancestorWeb/.
Diallo
Abdoulaye Banire
AB
Department of Computer Science, Université du Québec à Montréal, PO. Box 8888 Downtown Station, Montreal, QC H3C3P8, Canada. diallo.abdoulaye@uqam.ca
Makarenkov
Vladimir
V
Blanchette
Mathieu
M
D000818:Animals; D001483:Base Sequence; D002874:Chromosome Mapping / Q000379:methods*; D016678:Genome / Q000235:genetics*; D006801:Humans; D020407:Internet; D008969:Molecular Sequence Data; D010375:Pedigree; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*